Civil War: Indonesia (1975-1999)

Kenneth Ray Glaudell. Civil Wars of the World: Major Conflicts since World War II. Editor: Karl DeRouen Jr. & Uk Heo. Volume 1, ABC-CLIO, 2007.

Country Background

The Indonesian archipelago covers an ocean area the size of the continental United States. Of its 17,000 islands, 6,000 are inhabited. Its landmass is concentrated on four islands (Java, Sumatra, most of Borneo, and half of New Guinea); most Indonesians reside on Java. Its second most populous island, Sumatra, was the main site of the catastrophic December 2004 tsunami. Indonesia shares three islands with other governments. Borneo is shared with Malaysia and Brunei. New Guinea is shared with Papua New Guinea. The island of Timor is shared with newly independent East Timor. These islands—and many others—all have experienced civil strife. Indonesian land frontiers include Malaysia (1,100 miles of border), Papua New Guinea (500 miles), and East Timor (140 miles of frontier on an island only 250 miles by 50 miles). It is on Timor that Indonesia’s most significant civil war occurred.

Geography plays a significant role in Indonesia’s civil wars. Indonesia stretches 3,000 miles east to west and 1,000 miles north to south. Spread over 3 million square miles of ocean, the land area is 700,000 square miles. Of this land, 10 percent is cultivable, with another 7 percent under permanent crops. The remainder includes crowded Javanese cities and uninhabited steep mountains in eastern Papua. Mineral deposits (gold, copper) are found in the east, and oil and natural gas are concentrated in the far west (Aceh), the east (Papua), and other peripheral areas. In the outer islands, insurgencies take the form of traditional guerrilla movements, using the Cuban-style foco (Spanish for “focus”). On densely crowded Java, where most Indonesians live, however, violence takes the form of classical terrorism, including bombings, abductions, and murders. This tendency toward terrorism and away from traditional guerrilla tactics also prevails on the smaller islands, such as Sulawesi and the south Malaccas.

Indonesia’s economy is linked to the surrounding seas. This determines its cultural complexity as well as the integration of its local civil wars with wider regional movements and even global violent nonstate actors such as al-Qaeda. Seaborne trade has linked the archipelago with the world for 2,000 years. Consequently, the cultures of neighboring Asia have exercised influence on what would become Indonesia since antiquity. Although Buddhism prevailed in the area, by 1364 the Hindu kingdom of Java had conquered much of future Indonesia.

Java’s rulers came into contact with Islam in the twelfth century. Islam as a cultural-political force predominated in Java and Sumatra by the late 1500s. Simultaneously, Christian proselytizing took place in the east with the arrival of Portuguese and Dutch elements. Modern sectarian struggles on Indonesia’s Outer Islands are simply the most recent manifestation of the coincidental arrival and subsequent clash of Islamic and Christian polities in the Indonesian archipelago in the 1500s.

Although most Indonesians profess Islam, earlier Buddhist and Hindu traditions still persist, and some ethnic groups retain their Catholic or Protestant traditions. Additionally, the folk culture of many nominally Islamic ethnic groups in Indonesia contains significant pre-Islamic elements. Many on the Outer Islands have retained their animist cultures in isolation from the earlier Buddhist-Hindu polities or later monotheistic missionaries.

The diversity of Indonesia has serious security consequences and is a source of its high number of intrastate wars. Ambon, central Sulawesi, Kalimantan, and East Timor illustrate this. All have been the site of recent clashes. The reinforcing cleavages of language, race, and religion in Indonesia today are partially ameliorated in many regions by the complex intermingling of belief systems in popular culture, as well as by the internal divisions of the otherwise predominant religion, Islam.

As religion is at the heart of many of Indonesia’s civil wars, the nature of the country’s religions must be explored. Indonesian Muslims have historically been identified as either abangan (a Javanese term for Muslims influenced by pre-Islamic folk cultures) or santri (“pure” or “white” Muslims—those committed to Islamic orthodoxy). In its extreme form, the abangan tradition shades into kebatinan—an amalgam of Hindu, Buddhist, and Sufi (mystical Muslim) traditions given official recognition in the 1945 constitution, which created a Department of Religious Affairs to oversee “legitimate” Indonesian religious traditions. Interestingly, the kebatinan tradition is not subject to the oversight of that department but is under the Department of Education and Culture.

Although Muslims on Indonesia’s margins— those most likely to be living as minorities within non-Muslim communities, as on the (historically) largely Christian Malaccan islands—are more likely to be santri, the dominance of abangan culture within Java’s population and especially among its elites has meant that the Indonesia state has not been amenable to the imposition of stricter Islamic laws.

An exception to Indonesia’s tolerant vision of Islam is on Sumatra, in the area called Aceh. Northern Sumatra has long been a hotbed of political tension between both santri and abangan Islam as well as between Muslims and non-Muslims. Almost immediately after achieving independence, the secularly inclined and nationalist-leftist Indonesian government faced an Islamist insurgency in Aceh (known as the Darul Islam movement). Prior to the 2004 tsunami, Aceh still presented one of Indonesia’s most significant security threats.

Indonesia’s demographic parameters are complex. Islam is professed by 88 percent of the population, but only 15 percent idealize an Islamic state. Only 2 to 4 percent of Indonesians are sympathetic to the most prominent radical Islamist group, Jemaah Islamiyah (Islamic Association [JI]), or to similar groups such as Laskar Jihad (Army of Jihad), the umbrella group Front Pembela Islam (Islamic Defenders Front), and Hizbullah (“Party of God”; not to be confused with the similarly named Lebanese group— Hizbullah was founded with Japanese support during World War II [Lapidus 1988, 770]).

Ethnic identity and religious affiliation are interwoven. Many intrastate conflicts could as easily and as accurately be described as racial, ethnic, or nationalist in structure as they could be confessional. Ethnically speaking, the single largest segment of the Indonesia population is Javanese, at 45 percent. The next largest group, Sundanese, constitutes less than 15 percent. No other group exceeds 10 percent of the population. Language is coterminous with ethnicity, with the official tongue, Bahasa Indonesia, serving as a lingua franca. Bahasa Indonesia was created as a simplified version of the Malay language. In their homes, most Indonesians continue to use their local dialect (most commonly Javanese).

Below the surface of the religious-communal and ethnic-linguistic contours of Indonesia’s civil wars, the impact of colonial history is clearly discerned. The history of Indonesia’s integration into a European-dominated global political system began in the 1500s with the arrival of Portuguese explorers. During the 1600s, the archipelago came under Dutch control, except for East Timor, which remained under Portugal’s authority until 1975. Under Dutch rule for three centuries, Indonesia was known as the Netherlands East Indies, or NEI. Originally colonized for its role in the spice trade, Indonesia evolved economically under colonialism to become a major supplier of coffee, sugar, tea, and other cash crops. Its role as a producer of petroleum emerged late in the colonial era.

This recent development has fueled Indonesia’s insurgencies in some cases. Major petroleum and gas deposits in northern Sumatra are at the heart of Acehnese separatists’ objections to continued Javanese domination. Eastward, the harvest of timber and gold (along with exploration for fossil fuel deposits) has brought environmental degradation at the hands of outsiders (largely Javanese) to Papua and has helped to stoke local resistance to their continued control over the area. Petroleum deposits in the seas lying between Timor and Australia were reputed to be a motivator for Indonesia’s initial occupation of East Timor in 1975, as well as its reluctance to relinquish control of the territory.

The primary significance of Dutch colonial policy in Indonesia was the geopolitical impact of the creation of the NEI. Without the Dutch conceptualization of this archipelago as a single entity, the many conflicts engendered by separatist aspirations, transmigrating populations to the Outer Islands, and conflicts over resources would simply not exist. Prior to Dutch rule, no state had controlled the entire archipelago. At most, the Javanese managed to control their home island, the bulk of Sumatra, and a handful of Outer Islands. Dutch colonial rule gave final shape to what would become Indonesia, laying the foundations for cycles of separatism, mass migrations, and violent economic struggles. The extent of the former NEI precisely defines the borders of Indonesia today.

In the late 1800s, an independence movement evolved in Indonesia. This group was composed mostly of Javanese-speaking middle classes. Although this initial movement stalled, World War II and the Japanese occupation of the NEI gave Indonesian nationalists an opportunity to push for independence. A group under Sukarno (many Javanese go by only one name) and Mohammad Hatta declared the establishment of the Republic of Indonesia in August 1945, three days after occupying Japanese forces surrendered to the Allies.

Holland struggled to regain control of Indonesia but encountered resistance from nationalists, now armed with abandoned Japanese weaponry. In 1949, the hostilities between the Netherlands and Indonesians ended, with sovereignty transferred to an Indonesian government. In 1950, Indonesia gained United Nations recognition. Indonesia was to have a violent relationship with both its neighbors and its own minorities. Although competitive political parties and sporadic elections have characterized the country’s governmental structures since independence, it has more often been seen as “not free” or “partly free” by the democratic evaluation systems employed by Freedom House. During East Timor’s insurgency, Indonesia was rated “partly free.” There was slight improvement in political rights and civil liberties scores from 1974 (the year before the war in East Timor) to 2004 (five years after East Timor’s UN occupation). Since 2000, the Indonesian government has been rated “partly free,” with scores of 3 on political rights and 4 on civil liberties. In the year preceding the Indonesian invasion of East Timor and the subsequent violent separatist struggle, the government was rated 5 on both political rights and civil liberties, giving it the same “partly free” designation from Freedom House (Freedom House 2005).

Economic growth in Indonesia has been remarkable. Although reliable data for the early years of separatist movements and other insurgencies do not exist, for the longest running of the current struggles (Papua-Irian Jaya), Indonesia’s real gross domestic product per capita has improved from $902.74 (in constant 1996 US dollars) in 1965 to $3,637.30 in 2000. This is fourfold growth over thirty-five years. Much expansion followed the 1973-1974 surge in oil prices, when per capita GDP jumped 25 percent in two years. Comparing Indonesia’s performance in macroeconomic terms from the era just before the occupation of East Timor (1974) to Indonesia’s departure in 2000, the growth is impressive: from $1,349.50 per capita to $3,637.30 per capita. That latter number masks the decline caused by the Asian financial “meltdown” of the late 1990s. Prior to the collapse of the value of the Indonesian rupiah, GDP per capita peaked at $3,989.84 in 1997. Just one year later, it had dropped to $3,525.65, a fall of almost $500 per person, or 11.6 percent (Heston, Summers, and Aten 2002).

Oil is Indonesia’s most valuable and exportable resource, and the country is unique among members of the Organization of Petroleum Exporting Countries (OPEC) in its status as a net oil importer. In part, Indonesia became a victim of its own success. The massive economic growth of Indonesia in the late 1970s through mid-1990s led to increased domestic demand for oil. This was not the only factor shaping the country’s loss of oil revenue. Indonesia’s aging infrastructure and a lack of investment during the chaotic 1990s were contributing factors. With a surge in oil prices since 2003, investment may be increasing, leading to heightened production and a return to net petroleum exporter status. For Indonesia’s poor (17 percent lived below the poverty line in 1998), the 1997-1998 decline was calamitous. This has implications for separatist sentiments in the Outer Islands, as poverty rates rise the farther one goes from Java. Papua, for example, has a poverty rate ten times that of Jakarta.

The financial meltdown of 1997-1998 spelled the end of over three decades of one-man, one-party rule by President Suharto and his Golkar political movement. The weakness of the central state caused by this economic dislocation coincided with Jakarta’s decision to bow to international pressure and allow a plebiscite on possible independence for East Timor. Whether the economic stabilization of Indonesia or the recent surge in oil prices can help the central authorities prevent the loss of further restive Outer Island provinces is an open question. Gains realized from post-2000 economic growth have been offset by massive destruction and death brought by the 2004 tsunami.

Ironically, it may have been the tsunami itself that extinguished any realistic Acehnese separatist hopes of a Timor-like victory, as most of Indonesia’s tsunami-related losses occurred in Sumatra’s insurgent heartland. Banda Aceh, presumptive capital of a would-be independent Aceh, was leveled by the deadliest natural disaster in modern human history, which took the lives of 220,000 Sumatrans (127,000 confirmed, more than 93,000 missing). Those left homeless numbered 441,000, and $4.5-$5 billion in property was destroyed (CIA 2006b). The destruction of Aceh might weaken the central government sufficiently to embolden separatists in Papua province and eventually in Kalimantan as well. The economic dislocation of the country may also fuel an increase in support for radical political movements critical of the central government’s inability to cope with the challenges of the tsunami. In particular, the radical Islamists of JI hope to profit politically from the 2004 disaster.

Conflict Background

Using widely accepted conflict list calculations, Indonesia has seen six civil wars (Fearon and Laitin 2003). However, of Indonesia’s many conflicts, only the Timorese struggle has resulted in a rebel victory. The remaining rebellions were either successfully quashed by Indonesian authorities or remain unresolved conflicts at this time.

The other major civil wars of Indonesia must be understood if the full significance of the Timorese separatist struggle is to be grasped. In chronological order, these civil wars are the Republic of South Molucca movement (1950); Darul Islam I (1953); Darul Islam II (1958-1960); the Free Papua Movement, or Organisasi Papua Merdeka (OPM) (1965-present); and the Free Aceh Movement, or Gerakin Aceh Merdeka (GAM) (1991-present). Additionally, widespread violence has beset the Indonesian archipelago from its independence. Among the more significant were the 1965 attempted coup and 1966 change in leadership from Sukarno to Suharto, which led to the violent suppression of the Indonesian Communist Party (PKI) and alleged sympathizers of the Beijing-affiliated party.

The repression of PKI left at least 78,000 and perhaps as many as 2 million dead. Before Sukarno was driven from power, he promoted a series of violent actions against neighboring states, most notably the Konfrontasi (“confrontation”) against Malaysia on the island of Borneo. This struggle between ethnic Malays, indigenous Dayaks, and transmigrating Javanese and Madurese on Borneo evolved from a state-led proxy war between Indonesia and Malaysia into a cycle of civil strife that the authorities in Jakarta have struggled to defuse. Violence, largely along the Dayak-Madurese divide, remains intractable. Indonesian military forces have been repeatedly redeployed from other troubled areas of the archipelago to quell disturbances in Kalimantan.

Currently, the government is facing a nationwide radical Islamist challenge from a variety of groups. The most notable of these is the Jemaah Islamiyya. It is linked to Indonesia’s worst single act of terrorism, the 2002 Bali bombing that killed more than 200, as well as to smaller acts of violence and campaigns of civil unrest on Java and the Outer Islands. Some Outer Islands violence is linked to another radical Islamist group, Laskar Jihad. Each of these five civil wars is examined to shed further light on the complexities of Timor’s conflict.

The Republic of South Molucca (Maluku) Movement (1950)

Indonesia was beset by internal conflicts from its inception. During the period 1941-1945, Indonesia was under Japanese occupation. Japanese occupying forces, upon surrendering in 1945, allowed their weapons to be taken by Indonesian nationalists. Anglo-Australian troops were the first Allied units to arrive in the region. They soon found themselves at war with the locals. Dutch authorities tried to reimpose control but were only partially successful. By 1947, they had come to terms with the nationalists, creating a half-independent Indonesia. Java and Sumatra constituted an independent republic, whereas the Outer Islands joined the Netherlands-Indonesian Union with joint Dutch, Outer Island, and republican (i.e., Javanese-Sumatran) affiliations.

This arrangement was dubbed the Republic of the United States of Indonesia (RUSI). It was doomed from the start. In its first months, there was an uprising in the Malacca islands (by a group of largely Christian separatists). The Republic of South Maluku (RMS) was proclaimed in Ambon in April 1950 by former members of the now-defunct Royal Netherlands Indies Army (KNIL). Malaccan Christians had formed an integral part of the colonial forces used to control Java, Sumatra, and other Muslim-majority areas of the Netherlands East Indies (NEI). These forces felt threatened by the new political order. Although this group of ex-soldiers and police had initial advantages in the rebellion, sheer force of numbers crushed the RMS, and thousands of South Malaccans went into exile. This clash was the opening salvo in an ongoing struggle between the forces of centralization of power in Jakarta and the demands of the geographic and ethnic peripheries of the country.

The Darul Islam Movement I (1953)

Shortly after the repression of the RMS, a group describing itself as the Darul Islam movement in western Java, northern Sumatra, and southern Sulawesi challenged state authority. The phrase Darul Islam refers to the Islamic conception of a properly constituted polity. In theory, the whole of the Muslim-majority world should be structured into a single entity under Islamic law. Such a state is the “abode of Islam”—in Arabic, Darul Islam. Everything else is Darul Harb—the “abode of war.” Several nationalists who had previously helped expel the Dutch now sought an Islamic state. Such attitudes were most prevalent in northern Sumatra but also existed among small santri Javanese Muslim communities. The Darul Islam movement’s founder, Dekarmadji Maridjan Kartosoewirjo, began his movement in earnest in West Java in 1948. In August 1949, he declared an Islamic State of Indonesia. He proclaimed himself imam (“leader”) of this new political system and announced a state of jihad between Darul Islam and the Republic of Indonesia. His goal was clear: “God willing, this Holy War or Revolution will continue until… the laws of Islam apply perfectly throughout the Islamic State of Indonesia… At this time the National Independence Struggle, which has been attempted for almost four years, has broken down” (Riddell 2005, 162).

Kartosoewirjo argued that the secular ideology of Sukarno was failing in its efforts to oust Dutch colonial influence and that only a truly Islamic state could succeed. In fact, the Dutch were on the verge of defeat, and Sukarno was about to assume full control over the entire former NEI. Kartosoewirjo hoped to prevent the secularists from consolidating power. His movement succeeded in temporarily seizing West Java plus portions of Sumatra (especially Aceh). Many of Darul Islam’s leaders were from the original Indonesian armed forces, giving the first phase of the rebellion a peculiarly internecine aspect. Some of its military leaders were co-opted by the Indonesian state, and its original political base in West Java was quickly intimidated into submission. Pro-Darul Islam attitudes persisted in peripheral areas, especially in Aceh. After the initial suppression of the Darul Islam movement in 1953, it flared up again—this time with less Javanese participation and more Acehnese support—in 1958.

Darul Islam II (1958-1960)

Although the Army captured its main centers of operation in 1960, it continued to threaten the organs of state power at a lower level until its leader was captured in 1962 (Huxley 2002, 31). This second manifestation of Darul Islam was part of a countrywide uprising that was only partly Islamist. It was fueled by the increasing closeness of the Indonesian Communist Party (PKI) and Javanese abangan syncretism to the rule of Sukarno, leading to a rapprochement between secular-nationalist Army elements and civilian Islamist political parties, along with ethnie minorities fearful of Javanese domination of the Outer Islands. These disparate forces (nationalist-secularist elements in the army, Islamists, and minorities) made common cause in their resistance to Sukarno and his Marxist and Javanese power bases.

The outcome was a complex uprising referred to as the second Darul Islam movement. A rival provisional state was established by an array of armed factions, including forces in locations as far apart as Ambon and Sumatra, while President Sukarno was on a trip to Thailand in 1958. Although it initially received covert aid from some U.S. elements (flying American-built aircraft out of the Philippines and Taiwan using Chinese, Filipino, and American pilots), its lack of success led to a shift in U.S. official attitudes, with Jakarta ultimately receiving U.S. backing. The combined Darul Islam rebellions and civil disorders produced roughly 40,000 fatalities and lasted fifteen years, counting from the emergence of the movement prior to Kartosoewirjo’s first declaration of an Islamic state in 1948 to the capture and executive of the imam in 1962 (Riddell 2005, 162-63). Following these internal pseudo-civil wars, Sukarno turned his attention outward.

The Free Papua Movement, or Organisasi Papua Merdeka (OPM) (1965-Present)

At the time of Indonesia’s independence, the Dutch-ruled half of New Guinea remained under Dutch control. Colonial authorities permitted the region some autonomy to forestall support for liberation via Indonesian occupation. In reality, few indigenes would have welcomed Indonesian occupation. To gain control of the region, Indonesia’s nationalistic rulers negotiated with the Netherlands but failed to achieve their aim, the unconditional annexation of what they then called Irian Barat. Conflict with Dutch authorities ensued in 1961. In August 1962, an agreement was reached for the Jakarta government to assume administrative responsibility for Irian Jaya by May 1963.

In 1969, under UN supervision, the Indonesian government conducted an “Act of Free Choice” in Irian Jaya. A handpicked group of 1,025 Irianese representatives of local councils agreed to remain part of Indonesia. Then the UN General Assembly confirmed the transfer of sovereignty to Indonesia. This was followed by sporadic guerrilla activity. Resistance was light, but with increasing immigration of non-Papuans, tensions with indigenes increased. This process was exacerbated by increased politicization of religious identity in Indonesia. Since the downfall of President Sukarno and his successor, B. J. Habibie, there have been more explicit (and militant) expressions within Irian Jaya of its indigenes’ desire for independence. The OPM (Organisasi Papua Merdeka, or Free Papua Movement), has been waging a low-intensity struggle for more than three decades. The OPM evolved out of the Papua Youth Movement, a group that had opposed Indonesian occupation since its inception in 1962. The power of the OPM is significantly constrained by the tribal nature of Papuan society. By the mid-1990s, immigrant non-Papuans constituted one-third of Irian Jaya’s population—and the emerging importance of the Freeport mine (a gold and copper extraction establishment, founded in 1972) to the Indonesian economy— meant that prospects for Papuan secession were at perhaps their lowest point. The OPM was reduced to operating in two rival bands working from inside the territory of Papua New Guinea on Irian Jaya’s eastern frontier (Huxley 2002, 43). One estimate had only 200 hardcore OPM warriors (Rabasa and Haseman 2002, 107). The government of Papua New Guinea was far more concerned with maintaining diplomatic ties with Indonesia than with promoting the welfare of its ethnic kin in Irian Jaya, so its support for OPM forces working from its remote western highlands has been limited.

OPM received a new lease on life when the long-standing Suharto regime, in power since 1966, began to falter under the strains induced by the Asian financial crisis of 1997-1998. As the Timorese independence movement gained momentum, as the Acehnese insurgents became more active, and as the various Islamist militant organizations engaged in acts of violence against non-Muslim minorities and central authorities, the OPM and the broader Melanesian separatist community saw an opportunity to achieve greater autonomy or independence and escalated their activities. Even some traditional Melanesian tribal leaders who had been complicit in the pro-Jakarta Act of Free Choice signed onto the separatist cause (Huxley 2002, 43). Although the OPM had engaged in relatively small, symbolic acts of violence, with rare hostage takings designed to disrupt important Indonesian economic functions and help secure funding for the group, a much larger group now emerged with the as-yet-unrealized potential to directly confront the police and armed forces in Papua.

This new Satgas Papua (Task Force Papua) was composed of traditional tribal militias and could field as many as 22,000 armed men. With insurgent forces confronting them on several fronts, authorities made several concessions to the Papuan separatists. The provincial name was changed to Papua, and the local Morning Star flag (previously outlawed) was allowed to be displayed under limited circumstances as long as the national Indonesian banner was flown alongside it. These concessions convinced locals of the declining fortunes of Indonesian authorities, encouraging their heightened defiance of Jakarta. In one of several similar incidents, when local police cut down a Morning Star flag in the highland Papuan village of Wamena and killed some Satgas Papua militiamen, the group retaliated by killing several local non-Papuan settlers. As part of this escalating cycle of violence, Indonesian military forces began to arm and raise local immigrant militias. They followed this pattern in other separatist insurgencies as well, notably East Timor. The most prominent of these army-abetted, pro-Jakarta militias in Papua is the East Merah Putih force. It is reputed to have received support from the largest Islamist militant group in the country, Laskar Jihad, including roughly 100 trained fighters. Some of these may have been trained in Afghan and Pakistani Jihad training camps affiliated with al-Qaeda (Riddell 2005, 170).

Between the onset of Indonesian pressure to control Irian Jaya and the UN’s conferral of sovereignty over that area on Jakarta, President Sukarno tried unsuccessfully to expand Indonesia in the opposite geographic direction. This led to the country’s one postindependence interstate war (although, notably, the Correlates of War project (Sarkees 2000). does not considerate it to be a true government-to-government military confrontation, the historical evidence seems to sustain that characterization of the conflict).

Borneo (1962-Present)

The Konfrontasi (“confrontation”), as Sukarno styled his efforts at expansion, began with the movement of British Malaya toward independence in the late 1950s. Although the history of the conflict is complex, a simple outline of its parameters must suffice. Malaya (the peninsular component of modern Malaysia) achieved independence in 1957. It comprised only a few of the several British colonies in the region, which also included Singapore and three territories on the northern side of the island of Borneo—Sarawak, Sabah, and Brunei. It should also be noted that the Philippines laid claim to the northernmost extremities of Borneo. A Communist insurrection in the area in the late 1950s, led mostly by ethnic Chinese subjects of Britain’s Malay territories, had been supported by Jakarta, although it was ultimately suppressed by British imperial forces, including Australian and New Zealand troops as well as local Malay units. Anxious to validate his nationalist, anti-Western credentials, and perhaps with one eye on the oilfields of Brunei, Sukarno sought to build up a movement within both British-controlled Borneo and mainland Malaya for Indonesia annexation.

Sukarno formed the North Kalimantan National Army (TKNU). This group launched a rebellion in Brunei in December 1962. TKNU’s goals were to seize the Sultan of Brunei (he escaped), the oilfields, and as many European hostages as possible. Within a week of the rebellion, British-led forces, including Gurkhas flown in from Singapore, reestablished control, and by April 1963 the TKNU leadership had been captured. With no effective forces left, Indonesian (and Filipino) authorities acquiesced in the formation of a Malaysian federation, contingent upon the holding of a referendum.

Covertly, however, Sukarno pushed for the arming of approximately 24,000 ethnic Chinese Malaysians (who, although primarily pro-Beijing communists, shared Jakarta’s antipathy for the new Malay state and its British mentors), and the Indonesian army infiltrated small units into Malaysian Borneo. Openly, Sukarno declared a Konfrontasi against the creation of a unified Malaysia state that included any portion of Borneo. Eventually, this activity escalated to include the employment of Indonesia army units within Sarawak and Sabah, as well as less frequent but well-documented small-scale operations on the Malay Peninsula, most notably in Johore.

In January 1965, two years into the Konfrontasi, Sukarno formally withdrew Indonesia from the United Nations in protest after Malaysia won a seat on the Security Council. By now, Sukarno had declared himself the champion of all emerging states that were struggling against the neocolonialists of the formerly British-led, and now U.S.-directed, West (which he saw as having created Malaysia as a means to encircle him and his greater Indonesian vision). He backed violent nonstate actors in pursuit of his foreign policy aims in the region. He created and deployed irregular militant groups across Borneo. He promoted the transmigration of Javanese and Madurese islanders to extend Jakarta’s control over peripheral areas in Borneo, Sulawesi, and elsewhere.

Finally, regular Indonesian army units served both in the Konfrontasi against Malaysia and Brunei and in the suppression of indigenous resistance by Dayak and Malay populations on Borneo to transmigration. Later, these forces were employed to keep the three warring populations apart. His successors pursued similar policies in Papua, Timor, and elsewhere. His ultimate failure to destabilize Malaysian Sabah and Sarawak can be attributed to several factors, including aggressive and proactive patrols of British, Australian, and New Zealand forces, who entered Kalimantan to ambush Indonesian forces before their infiltration into Malaysia. Additionally, domestic political developments in Java put a stop to Sukarno’s efforts to “crush Malaysia,” as he said in a July 1963 speech (Metcalf 2001, Appendix 4). For a variety of reasons, Sukarno lost power in a complex coup during 1965-1966.

The Year of Living Dangerously (1965-1966)

For years, Sukarno had played off his two domestic rivals (and supporters), the Indonesian Communist Party and the army. Additionally, Sukarno had to cope with various Islamist factions, almost all of whom were usually opposed to him, as well as additional internal and external political forces. Most significantly, the latter group included the People’s Republic of China, which backed the PKI, and the United States, which naturally opposed the same group. Poised between all these contradictory forces, Sukarno remained “president for life” (a self-conferred title). He created and enforced his own ideology (Pancasila, the Sanskrit word for “the five principles”: monotheism; just and civilized humanitarianism; nationalism; popular sovereignty; and social justice). It did seem that, in many ways, he was politically indestructible, given the apparent unity he imposed upon a hopelessly complex Indonesia and the remarkable way in which he convinced his followers to adhere to his self-contradictory philosophy. Presciently, he described the increasing tension within Indonesia as part of a “Year of Living Dangerously” in a famous 1964 speech.

Eventually, his juggling act failed, as he put the Army in jeopardy of defeat and humiliation in Kalimantan. It was clear that the leadership of the armed forces was becoming increasingly uncomfortable with Sukarno’s confrontational style. Conversely, lower-ranking officers (and especially air force, marine, and naval officers) were being exposed to PKI proselytizing. When communist-sympathizing officers seized some of their superiors and killed them, a complex whirlwind of political events transpired that to this day remain obscure. The details upon which everyone is in agreement are the starting and ending points of the coup—from the kidnapping of the generals in September 1965 to the installation of Suharto as acting president in March 1966. Everything in between those two events remains controversial. But in terms of political violence, the outcome was very clear: It led to the single largest loss of life in Indonesian political history with the possible exception of the subsequent East Timor independence struggle. Estimates of PKI members killed in the years after the coup attempt vary from 78,000 to 2 million (Metcalf 2001, 14-16).

From a regional security perspective, the upshot was that Suharto, now president, terminated the Konfrontasi—but he did not put an end to other long-cherished Indonesian nationalist goals. After all, it was he who finalized the Irian Jaya takeover in 1969, a year after he had been designated president, and a full three years after Sukarno had conferred upon him the title of acting president. Among his most significant acts of expansion was the absorption of East Timor.

East Timor (1975-1999)

Following the consolidation of Indonesian hegemony in Papua, Jakarta turned its attention to the last archipelagic European colony. East Timor had been a Portuguese colony from 1524 to 1975. Late in that year, an East Timorese independence movement with Marxist inclinations named Fretilin (the Revolutionary Front of Independent East Timor) declared the island’s independence. Nine days later, the Indonesian army seized the territory.

In 1976, Indonesia declared East Timor its twenty-seventh province; following the declaration and military occupation by the Indonesian army, there were widespread political protests and small-scale but relatively deadly guerrilla activity in the region by opponents of Indonesian rule. Unlike the seizure of Irian Jaya, which was sanctioned by the UN, international recognition of East Timor was not forthcoming. Although major powers acquiesced in the fait accompli, political pressure on (and in some cases, by) Western capitals to undo the conquest was persistent. A war of secession raged from 1976 until the arrival of UN-authorized Australian military forces in 1999. Even after that, the violence continued; pro- and anti-Jakarta militias within the Timorese population waged war on each other in refugee camps on the western (Indonesian) end of the island.

Like the OPM struggle in Papua, it was a secessionist war provoked by military occupation by an unwanted outside power on the heels of a European decolonization. Although the lead resistance group claimed a Marxist orientation and the population was overwhelmingly Roman Catholic, the struggle was neither ideological nor communal. Estimates of total casualties in the war vary widely. The largest, broadest estimates (such as the 100,000-250,000 cited by the CIA [2005b]) typically include direct battle deaths, political murders, disappearances, starvation, and disease. Narrower, more precise calculations are confined to battle deaths and publicly verified killings. Fearon and Laitin (2003) give low, high, and best estimates of 17,493, 61,170, and 33,658 respectively. The initial Indonesian invasion came on the heels of an intra-Timorese struggle.

As Portugal prepared to decolonize the island, the rival Marxist Frente Revolucionaria de Liberatação Nacional de Timor-Leste Independente (Fretilin) and non-Marxist Uniao Democratica Timorense (UDT) political movements fought. UDT called for union with Indonesia, and in response Fretilin declared an independent East Timorese state in November 1975. The UDT toppled this government by seizing control of the capital, Dili. In the midst of this chaos, the Indonesian military intervened with a force of 10,000 in December 1975. In the initial phase of the war, Falintil (the Armed Forces for the National Liberation of East Timor; Fretilin’s armed wing) fielded a force of indeterminate size that endeavored to directly confront the Indonesian military. They sought refuge in the hills, unable to wage sustained combat at the same level as the government. By December 1978, the main Falintil logistics bases on Mount Matebian had been captured by Indonesian forces. The wholesale surrender of Falintil cadres ensued, with only a rump guerrilla force left in the field. By 1983, Fretilin was reputed to have agreed to a truce with Jakarta, and in 1984 it ceased to maintain the legal fiction of the existence of an independent East Timor under foreign occupation.

All this took place in the context of the Cold War. The United States and its regional ally, Australia, saw an anti-Marxist Indonesia as critical to their security interests. Although it never publicly endorsed the Indonesian seizure of East Timor, the U.S. government maintained relatively close ties with Jakarta throughout this era. Australia’s parliament recognized the occupation as legitimate. With the end of the Cold War, the need to maintain Western ties to unsavory regimes lessened—and pressure to force a reversal of the occupation of East Timor increased. Although the violence of the early years of Indonesian occupation abated, low-intensity guerrilla conflict and heavy-handed counterinsurgency operations continued into the early 1990s. About one-third of all fatalities associated with the East Timor conflict occurred in the first two years of military operations. In the ensuing two decades, most deaths came from grinding poverty, allegedly deliberately induced famines, and occasional security force firings on demonstrations, funeral processions, and acts of nationalist defiance. Down from perhaps thousands of soldiers in 1975, the Fretilin-linked guerrilla forces may have numbered no more than 200 active armed persons by the 1990s. Its leader, Xanana Gusmao, was captured in 1992.

Sources: Doyle and Sambinis 2000; Fearon and Laitin 2003; “State Failure”; CIA 2006a, 2006b.
War: East Timor (Fretilin vs. Republic of Indonesia)
Dates: 1975-1999
Casualties: 33,658 (estimates vary up to 250,000)
Regime type prior to war: -7 (Polity 2 variable in Polity IV data—ranging from -10 [authoritarian] to 10 [democracy])
Regime type after war: 7 (Polity 2 variable in Polity IV data—ranging from -10 [authoritarian] to 10 [democracy])
GDP per capita year war began: $1,349.50 (constant 1996 US dollars)
GDP per capita 5 years after war: $3,500 (2004 estimate using 1996 constant dollars; 2004 East Timor income is $400 per capita)
Insurgents: Falintil, the armed wing of Fretilin; eventually, Fretilin forms umbrella group, CNRM (National Council of Maubere Resistance), which incorporates other rival insurgents such as the UDT.
Issue: Separatist movement; end Indonesian occupation
Rebel funding: Limited funds; Fretilin weapons come from Portuguese armories on Timor; UDT reputedly armed by Indonesia, at least initially.
Role of geography: Rebels retreat to highlands; diasporas in Australia and elsewhere support movement.
Role of resources: Offshore oil in Timor Sea may have driven Indonesian and Australian views on East Timor; Timor itself is resource poor.
Immediate outcome: 1999: UN-led occupation; Indonesian evacuation
Outcome after 5 years: 2002: East Timor independent; stable elections
Role of UN: Broker truce; negotiate plebiscite; UN peacekeepers
Role of regional organization: None in Timor; ASEAN oversees Aceh truce.
Refugees: 300,000 in initial stages of war; 200,000 in 1999
Prospects for peace: Favorable with continued UN/Australian presence
Table 1: Civil War in Indonesia

At this point, international pressure began to build; in 1997, when the economic situation in Indonesia deteriorated significantly, East Timorese separatists saw the opportunity to pressure Jakarta by appealing to its main creditors and trading partners. This led to UN-sponsored talks between Portugal and Indonesia, which produced a plebiscite on independence or continued association with Indonesia. In an abortive effort to promote the latter, pro-Jakarta militias, aided covertly by the military, waged a campaign of violence and intimidation. That only hardened Timorese voters’ resolve, precipitating a largely Australian intervention, with U.S. naval and air support, in 1999. On May 20, 2002, East Timor entered the United Nations as a sovereign state, theoretically bringing an end to the bloodiest of Indonesia’s many separatist, autonomous, and revolutionary civil wars.

The Insurgents

Fretilin (Frente Revolucionaria de Timor-Leste Independente: The Revolutionary Front for an Independent East Timor) was a Marxist party that came to prominence in East Timor in 1975 when the government of Portugal was toppled in a leftist coup. Officials in Lisbon wished to rid themselves of their colonial holdings and pushed for a quick transfer of power to like-minded political groups. A rival anti-Marxist party, the UDT (Uniao Democratica Timorense: Democratic Timorese Union) joined forces with a pro-Indonesia group to fight against Fretilin and its armed wing, Falintil (Forcas Armadas De Libertacão Nacional De Timor-Leste: The Armed Forces of National Liberation of East Timor). Falintil acquired its weapons from Portuguese arsenals, and had both a numerical and firepower advantage over its Timorese rivals. They hoped to acquire more material support from leftist governments around the world, but the relative isolation of East Timor and its proximity to hostile Indonesian and Western (Australian) forces made this impossible. There were scant resources on Timor to support any groups—the colony was among the poorest places in the world and remains so today, with a $400 per capita GDP.


Timor’s mountainous interior has often played a role in resistance to outside forces. This was true of the early days of colonial occupation. This was also the case during World War II, when Australian and Dutch forces landed on the island to slow the Japanese advance through the South Pacific. Many local Timorese aided them and applied what they learned when they began to resist the reassertion of Portuguese colonial authority after the war. When Indonesian forces arrived, Fretilin supporters were very quickly driven into the hills. Ultimately, however, the relatively small size of the island and the massive size of the Indonesian military deployment (at one point more than 20,000 regulars plus thousands of “Brimob” troops [mobile paramilitary police forces]) meant that the most remote reaches of the island, including the supply bases on Mount Matebian, came under Indonesian control.


Fretilin was quickly driven from populated areas by overwhelming force. Xanana Gusmao, who rose to the leadership of Falintil, called for a “protracted people’s war” in May 1976. This meant limited hit-and-run tactics. The Indonesian government forcibly relocated 200,000 Timorese to limit guerrilla access to communications and outside support. A “fence-of-legs” offensive was launched by the army to sweep the island of Falintil forces—but their relatively small size, plus their willingness to melt back into the population and cease violent activities, rendered this operation comparatively unsuccessful. It did, however, produce a drop in the number of violent Falintil attacks on army and police targets. Armed largely with older Portuguese weapons (including M-16 [AR-15] assault rifles, Belgian-produced FN assault rifles, and even obsolescent M-1 Garand rifles from World War II), Falintil was capable of only modest ambush attacks that occurred sporadically over the next twenty years. A typical tactic was to have a guerrilla dressed as a regular army soldier divert a truckload of Brimob police or Indonesian troops onto a roadside, where the vehicle would be attacked with grenades and the occupants gunned down. To avoid such attacks, the Indonesian army developed the policy of avoiding remote upland areas. These containment areas in rural Timor were cordoned off from the rest of the island while authorities tried to transform the civilian side of Timorese life. To this end, transmigration of non-Timorese to Dili and other areas on the island was undertaken.

The real success of Fretilin came with the development of an umbrella organization that embraced its former rivals, such as the UDT. The arrival of new, activist Bishop Belo, who would ultimately win the Nobel Peace Prize for his efforts, along with an international propaganda campaign against Indonesian occupation, eventually bore fruit. A papal visit further heightened global awareness of Timor’s problems, and although low-level violence continued to be perpetrated by Fretilin, the level of retaliatory violence by authorities lent further credibility to the Timorese cause. In the end, the separatists’ victory would be as much a product of public relations as of violent resistance.

Causes of the War

The cause of the war in East Timor was the Indonesian occupation of a culturally distinct area a majority of whose residents did not wish to be occupied by Indonesia. The question of whether the war constitutes a “sons of the soil” type of struggle is difficult. The typical “sons of the soil” war involves a peripheral minority and state-supported migrants of a dominant ethnic group. At one level, this describes Timor precisely. However, the fact that East Timor is a detached island limits the volume of majority migrants from the ethnic core of the state. This would lead one to expect it to be a lengthy war. Yet the absence of valuable contraband (a source of conflict prolongation) and the anticolonial nature of the struggle (East Timor shifted directly from Portuguese colony to Indonesian-occupied territory) should point in the direction of a speedy resolution to the conflict. What can be said with certainty, however, is that it is one of just a small handful of successful separatist insurgencies of the post-World War II era.


Conflict Status

The war has officially ended. Most of the 300,000 refugees generated by the most recent round of violence have been repatriated, although perhaps 20,000 remain in camps in Indonesian West Timor. Converting the various guerrilla factions into functioning members of society is difficult, and reconciling violently pro-Jakarta militiamen to the political reality of Timor has been even harder. An Australian-manned UN military mission will need to remain for the foreseeable future. None of these problems detract from the salient fact of East Timor: It is one of a mere handful of successful secessionist movements in the modern era.

Duration Tactics

Compared to other secessionist wars, the struggle in Timor was relatively short. After all, most secessionists never succeed. But the loss of life during the twenty-four-year occupation by Indonesia may have made it seem like a long-running war. The key element fueling Timorese determination to achieve independence may have been the harsh living conditions, severe poverty, and lack of alternative outlets for refugees that characterized life for the islanders. Unlike victims of similar aggression elsewhere, they had no alternatives. Unlike most people, they literally had nothing to lose but their lives. Given these dire conditions, it is not surprising that they fought so hard with so little to achieve their independence.

External Military Intervention

Although Timorese nationalists claim that the United States authorized the Indonesian invasion and abetted it by maintaining military ties with Jakarta, the latter is the extent of American involvement. The most significant outside intervention element in the war prior to the UN-Australian occupation in 1999 was the Indonesian military’s decision to “outsource” the repression of separatists to local, covertly armed militia groups. These groups went on a rampage that destroyed 70 percent of Timorese buildings and economic assets during the August 1999 referendum. The absence of outside involvement may have encouraged Indonesian seizure of Timor, but the presence of superpower involvement in 1999 also brought that intervention to an end.

Conflict Management Efforts

The first mediation efforts related to East Timor preceded the Indonesian invasion. Portugal tried to convene a meeting of all anticolonial movements on the island in their colonial enclave of Macau. The effort failed because Fretilin refused to attend. The chaos that ensued in Dili precipitated Indonesian intervention. From that point, UN resolutions called repeatedly for Indonesia to relinquish control of East Timor, but to no avail. When, however, the UN called for Portugal and Indonesia to work out a resolution to the crisis in the late 1990s, the effort was almost immediately successful. One key element in this success was the severe economic crisis confronting Indonesia. Desperately in need of IMF and bilateral assistance, Jakarta authorities had to accede to the demands of the United States and other powers, who wished to see a peaceful resolution of the lingering crisis. Once Portugal and Indonesia had worked out the details of the plebiscite, army-sponsored covert militias embarked on a campaign of violent intimidation in East Timor. At least some of the authorities in Jakarta were not reconciled to the loss of the territory. The violence of these militias was counterproductive—prompting more Timorese support for independence as well as provoking a UN Security Council-authorized military intervention by Australia, the United States, and others.


During the Asian financial crises of the late 1990s, Timorese separatists found additional international recognition in the form of a Nobel Peace Prize for their leaders, and finally Jakarta grudgingly succumbed to international pressure. After UN involvement in January of 1999, Indonesia agreed to allow the people of East Timor to choose between autonomy and independence by direct ballot. Efforts by state-enabled, if not centrally controlled, antisecessionist militias, meant to intimidate the islanders into voting to remain part of Indonesia, backfired.

In August 1999, the East Timorese population voted overwhelmingly for independence, with 98.6 percent of eligible voters going to the polls and 78.5 percent of them casting a pro-independence vote in the midst of violence that killed thousands and left East Timor in ruins. Today, East Timor has most of the trappings of statehood, but it is only through continued UN-authorized military force that it retains its independence. Absent a significant (largely Australian) armed deterrent, it is highly likely that vengeance-minded, pro-Jakarta militias (such as the Red and White Iron Militia) would wreak havoc from their bases on the western end of Timor.

Peaceful elections, a new constitution, and economic reconstruction are only part of the story of East Timor. Its greater significance may lie in whether it is a harbinger of things to come in other outlying Indonesian regions. With ongoing insurgent activities in Papua, a nationwide low-level radical Islamist campaign across Indonesia, a tsunami-impacted Acehnese separatist insurgency on the decline, and lingering interethnic violence in Borneo, Sulawesi, Maluku, and elsewhere, the authorities in Jakarta have much to fear if an independent East Timor proves to be a notable success story. The success of Fretilin, Xanana Gusmao, and the forces for Timorese secession may have an impact far beyond their own statehood.