Evidence for the ancient habitation of Indonesia was discovered by the Dutch paleontologist Eugène Dubois in 1891; these fossil remains of so-called Java man ( Pithecanthropus erectus ) date from the Pleistocene period, when Indonesia was linked with the Asian mainland. Indonesia's characteristic racial mixture resulted from at least two waves of invasions from South China by way of the Malay Peninsula and from intermarriage of these Indonesians with later immigrants, especially from India. The important population groups of today trace their descent from the immigrants of the second wave, which occurred around the 2nd or 3rd century BC . They subjugated and absorbed most of the other inhabitants. Indian influences permeated Java and Sumatra from the 1st to the 7th century AD . During this period and extending into the 15th century, local Buddhist and Hindu rulers established a number of powerful kingdoms. Among the most powerful of these was the Buddhist kingdom of Srivijaya, established on Sumatra in the 7th century; it prospered by gaining control of trade through the Strait of Malacca. To the east, in central Java, the Sailendra dynasty established its Buddhist kingdom in the 8th century. Relics of Sailendra rule include the great temple of Borobudur, Asia's largest Buddhist monument, with hundreds of bas-reliefs depicting the life of Buddha. Succeeding the Sailendra dynasty in 856 were followers of the Hindu god Shiva; these Shivaites built the great temple at Prambanan, east of Yogyakarta. Other Hindu kingdoms subsequently extended Indian influence eastward into east Java and Bali. The last of these was the Hindu kingdom of Majapahit, which was at the height of its power during the 13th century, when Marco Polo visited Java and northern Sumatra. When Majapahit collapsed around 1520, many of its leaders, according to tradition, fled to Bali, the only island in Indonesia that retains Hinduism as the chief religion. Even before Majapahit disintegrated, Muslim missionaries, probably Persian merchants, had begun to win much of the archipelago for Islam. About this time, also, the first Europeans arrived, and the first Chinese settlements were made. The Portuguese captured Malacca (Melaka), on the west coast of the Malay Peninsula, in 1511 and established control over the archipelago.
Dutch ships visited Java in 1596. The Dutch came in increasing numbers and soon drove the Portuguese out of the archipelago (except for the eastern half of the island of Timor), beginning nearly 350 years of colonial rule. The States-General of the Dutch Republic in 1602 incorporated the East Indian spice traders as the United East India Company and granted it a monopoly on shipping and trade and the power to make alliances and contracts with the rulers of the East. By force and diplomacy, the company thus became the supreme ruler of what became known as the Dutch East Indies. However, maladministration and corruption weakened the company after its early years of prosperity, and the Dutch government nullified its charter in 1799 and took over its affairs in 1800. The British East India Company ruled the Indies during the Napoleonic wars, from 1811 to 1816. During this period, Sir Thomas Stamford Raffles became governor of Java. When Dutch rule was restored, the Netherlands government instituted the "culture system" on Java, under which the Javanese, instead of paying a certain proportion of their crops as tax, were required to put at the disposal of the government a share of their land and labor and to grow crops for export under government direction. From a fiscal point of view the system was very successful, yielding millions of guilders for the Netherlands treasury, but this "net profit" or "favorable balance" policy fell under increasing moral attack in the Netherlands and was brought to an end about 1877. Thereafter, private Dutch capital moved into the Indies, but the augmentation of Dutch prosperity at the expense of Indonesian living standards was increasingly resented. With the adoption of what colonial administrators called the "ethical policy" at the beginning of the 20th century, the first steps were taken to give Indonesians participation in government. A central representative body, the Volksraad, was instituted in 1918. At first it had only advisory powers, but in 1927 it was given colegislative powers. An Indonesian nationalist movement began to develop during those years and steadily gained strength. Although retarded in the 1930s by the world economic depression, which was strongly felt in Indonesia, the movement revived during the Japanese occupation (1942–45) in World War II. A nationalist group under the leadership of Sukarno and Mohammad Hatta proclaimed an independent republic on 17 August 1945, adopted a provisional constitution providing for a strong presidential form of government, formed a revolutionary government, and resisted Dutch reoccupation. After four years of intermittent negotiations, frequent hostilities and UN intervention, the Netherlands agreed to Indonesian demands.
Sukarno became the first president of the new nation in 1949, and Hatta the vice president. Internal difficulties, fostered by a multiplicity of political parties inherited from Dutch colonial days, soon developed, and regional rivalries also threatened the unity of the new nation. Then as now, Java had some two-thirds of the country's population, but the great sources of wealth were found on the other, much less densely settled islands. Those living in the so-called Outer Islands believed too much governmental revenue was being spent in Java and too little elsewhere. After Vice-President Hatta, a Sumatran, resigned in December 1956, many in the Outer Islands felt they had lost their chief and most effective spokesman in Jakarta. Territorial army commanders in Sumatra staged coups and defied the central government; other rebel movements developed in Sulawesi. The government took measures providing for greater fiscal and administrative decentralization, but discontent remained, and the rebellions were put down by force. Thereafter, Sukarno bypassed parliamentary procedures and pursued an increasingly authoritarian, anti-Western policy of "guided democracy." In 1959, he decreed a return to the 1945 constitution, providing for a centralized form of government, and consolidated his control. On 27 December 1949, the Dutch recognized the independence of all the former Dutch East Indies except West New Guinea (Irian Jaya) as the Republic of the United States of Indonesia. A few months later, on 17 August 1950, the federal system was rejected and a unitary state, the Republic of Indonesia, was established under a new constitution. West New Guinea remained under Dutch control until October 1962, when the Netherlands transferred the territory to the United Nations Temporary Executive Administration (UNTEA). On 1 May 1963, Indonesia took complete possession of the disputed territory as the province of Irian Barat (West Irian); the province was renamed Irian Jaya in 1973. Indonesia, which aimed to acquire Sarawak and Sabah (which are on the island of Borneo with Kalimantan), opposed the formation of the Federation of Malaysia in September 1963 and announced a "crush Malaysia" policy. This policy was implemented by guerrilla raids into Malaysian territory that continued until August 1966, when a formal treaty was concluded between the two countries.
Communist agitation within the country and secessionist uprisings in central and eastern Java came to a head in the 30th of September Movement under the direction of Lt. Col. Untung. Sukarno, whose foreign policy had turned increasingly toward the Communist Chinese, may have had advance knowledge of the Communist-led coup attempt on 30 September 1965, which was directed against Indonesia's top military men; the coup was crushed immediately by the army, however, and in the ensuing anti-Communist purges more than 100,000 persons (mostly Indonesian Chinese) lost their lives and another 700,000 were arrested. By mid-October, the army, under the command of Gen. Suharto, was in virtual control of the country. On 12 March 1966, following nearly three weeks of student riots, President Sukarno transferred to Suharto the authority to take, in the president's name, "all measures required for the safekeeping and stability of the government administration." In March 1967, the People's Consultative Assembly (Majetis Permusyawaratan Rakyat—MPR) voted unanimously to withdraw all Sukarno's governmental power and appointed Gen. Suharto acting president. One year later, it conferred full presidential powers on Suharto, and he was sworn in as president for a five-year term. The Congress also agreed to postpone the general elections due in 1968 until 1971. Sukarno died in June 1970. On 3 July 1971, national and regional elections were held for the majority of seats in all legislative bodies. The Joint Secretariat of Functional Groups (Sekber Golongan Karya—Golkar), a mass political front backed by Suharto, gained 60% of the popular vote and emerged in control of both the House of Representatives (DPR) and the MPR.
In March 1973, the MPR elected Suharto to a second five-year term. Thus Suharto, with key backing from the military, began a long period of dominance over Indonesian politics. Under Suharto's "New Order," Indonesia turned to the West and began following a conservative economic course stressing capital development and foreign investment. In foreign affairs, Suharto's government achieved vastly improved ties with the United States, Japan, and Western Europe while maintaining links with the USSR.
On 7 December 1975, following Portugal's withdrawal from East Timor, a power struggle developed among various political groups, including the Revolutionary Front for an Independent East Timor (Frente Revolucionário de Este Timor Independente— Fretilin). The left-wing independence movement achieved military dominance forcing the Indonesian government to send troops into the former Portuguese colony and assume full control of the territory. On 17 July 1976, the Suharto government incorporated the territory as an Indonesian Province. This action was neither recognized by the UN, which called on Indonesia to withdraw and allow the Timorese the right to self-determination, nor accepted by Fretilin. Discontent with the Suharto regime mounted after the elections of 1977, in which Suharto's Golkar Party gained an overwhelming majority. The government acknowledged holding 31,000 political prisoners; according to Amnesty International, the total was closer to 100,000. Student riots and criticism of government repression resulted in further government measures: political activity was suspended, and leading newspapers were temporarily closed. Suharto was elected by the MPR to a third five-year term in 1978; during late 1977 and 1978, some 16,000 political prisoners were released, and the remainder of those detained in 1965 were released by the end of 1979. Golkar made further gains in the 1982 elections, and Suharto was elected for a fourth five-year term in March 1983.
To strengthen the government in the face of rising Muslim militancy, Suharto began to reestablish Sukarno as a national hero eight years after his death. Suharto called for greater loyalty by all political groups to the Pancasila ("five principles") framed by Sukarno in 1945. The credo encompassed belief in the one supreme being, humanitarianism, national unity, consensus democracy, and social justice. Muslim groups strongly objected to the new government program and organized demonstrations that took place in 1984 and 1985. The war against Fretilin continued into the 1980s, with reports of massacres by government troops and severe economic hardship among the Timorese. Negotiations with Portugal, still considered responsible for decolonization by the UN, began in July 1983. In Irian Jaya, the Organization for a Free Papua (Organisasi Papua Merdeka—OPM), which desires unification with Papua New Guinea and has been active since the early 1960s, increased its militant activities in 1986. The Indonesian Army (ABRI) continued to play a dual military and socioeconomic function, and this role was supported by legislation in 1988. Golkar made further gains in the 1987 elections, and Suharto was again reelected for a fifth five-year term in March 1988. During disagreements over nomination procedures for the vice presidency ABRI's influence was eroded.
Golkar sought to create national unity through its resettlement policies. From 1969–92, the Transmigration Program, a policy aimed redistributing population in Indonesia for political purposes and for demographic reasons resulted in almost 1,488,000 families moved from the Inner Islands to the Outer Islands. The Transmigration Program suffered from land disputes with local residents and environmental concerns over deforestation. The program alienated local populations and fueled ethnic conflict throughout the country. In Irian Jaya, the Free Papua Movement (OPM), attempted to sabotage the government's program that was turning the indigenous Melanesian majority into a minority. Indonesian troops attempting to capture Melanesian separatists would cross the border into Papua New Guinea. Indonesia and Papua New Guinea agreed to provide greater cooperation on security and trade issues and the leader of OPM, Melkianus Salossa, was eventually arrested in Papua New Guinea and deported to Indonesia and sentenced to life in prison in 1991. In 1989, tension from land disputes in Java and the Outer Islands produced social unrest that resulted in clashes between villagers and the armed forces. In 1990 an armed rebellion in northern Sumatra at Aceh arose over hostility toward government exploitation of mineral resources and its transmigration program. The government squashed the rebellion with a massive display of force.
Political openness was increasingly espoused during 1990–91 by political and labor organizations. In 1990 a group of prominent Indonesians publicly demanded that Suharto retire from the presidency at the end of his current term; in 1991 labor unrest increased with a rash of strikes, which the army was called in to quell. Government efforts to raise funds through a state lottery were opposed and finally forbidden on religious grounds when the country's highest Islamic authority declared the lottery "haram" or forbidden.
On 12 November 1991, during a funeral for a young Timorese killed in demonstrations against Indonesia's rule of East Timor, soldiers opened fire on the defenseless mourners provoking worldwide condemnation. Although the government took unprecedented steps to punish those involved, western governments threatened to suspend aid, and demands were made linking aid to human rights issues. The Netherlands' demand linking its aid to improvements in human rights was rejected when Suharto refused Dutch economic aid on 25 March 1992. In the aftermath of these events Suharto spoke at the Nonaligned Movement summit in Jakarta and to the UN General Assembly suggesting that developing nations needed to take a more prominent role in opposing North-South economic inequality. Suharto's challenge received a cool reception from Western nations, but it clearly signaled a reassessment of Indonesia's future international presence. In early December 1992 government forces captured Jose Alexandre (Xanana) Gusmao, leader of the Fretilin, who was hiding in Dili, in East Timor. On 21 May 1993 he was sentenced to life imprisonment. In late 1992, tensions between Muslims and Christians increased to the point of violence and vandalism of churches and mosques. Suharto requested that religious tolerance be practiced. By 1993 US policy toward Indonesia shifted toward criticism of Indonesia's rule in East Timor, and a threat to revoke trade privileges pursuant to Indonesia's treatment of the largest independent trade union, the SBSI (Indonesian Prosperous Labor Union). Adding further scrutiny to Indonesia's tarnished international image was a UN resolution on Indonesia's human rights violations placing the country on a rights "watch" list in 1993.
Although its total share of votes declined, Golkar won the 1992 elections, securing 282 of the 400 elective seats. In March 1993, Suharto was elected to a sixth term as president. Try Sutrisno, the commander in chief of ABRI, was chosen as vice president. Despite Golkar's victory, the country continued to experience economic and political difficulties. A major scandal occurred in March 1993 with the sale of $5 million in fake shares on the Jakarta Stock Exchange (JSE). In January 1994 President Suharto inaugurated 12 electric power plants with combined installed capacity of more than 2,000 MW. Violent labor unrest broke out in Medan in April 1994 with the mysterious death of a union activist. Ethnic Chinese, who are only about 3% of the population of Indonesia, were the target of demonstrators; one Chinese factory manager was killed. The success of the Chinese is widely envied and they are accused of exploiting the workers. On 21 June 1994 the government closed Tempo and two other publications by revoking publishing licenses. Tempo was accused of violating the journalistic code of ethics and pitting one person against another to the point where it affected national security based on its coverage of a controversial purchase of 39 warships from the former East German navy. Other publications were accused of more technical infractions including the failure to comply with registration procedures and publishing political and general news in spite of license restrictions limiting a popular tabloid's coverage to detective stories and crime stories.
Violent outbreaks, clashes, and riots increased in Indonesia from 1995–97. Riots between Catholics and Muslims broke out in East Timor in September 1995, leaving Dili's central marketplace in ashes. This was before Timor's Roman Catholic bishop, Carlos Filipe Ximenes Belo, and pro-independence advocate José Ramos-Horta shared the Nobel Peace Prize in 1996. Many incidents of rural unrest, including land disputes and ethnic strife, continued in 1995–96. The campaign for the 29 May 1997 elections was an unusually violent one, dubbed the "festival of democracy," as voters and demonstrators brought rocks, bricks, knives, machetes, and even snakes to the campaign. There was a ban on parades of trucks, cars, and motorcycles. This followed the uproar resulting from the ouster of Megawati Sukarnoputri as the Indonesian Democratic Party chairperson in June 1996. Her political involvement was seen as a rallying point for democratic change. Golkar took 74% of the vote in elections that were seen to be marked by fraud and over 200 people were killed during the campaign. The Muslim-oriented United Development Party (PPP) obtained 22%, and 3% went to the PDI.
In other violence, hundreds of lives were lost in a full-scale ethnic war in Kalimantan, as clashes between the Dayaks, the indigenous people of the area, and Muslim settlers from the island of Madora, broke out in December 1996. The fighting led to Malaysia closing part of its border with Indonesia in February 1997. In 1997, the country experienced the dual effect of increased ethnic conflict and economic decline. These twin forces were the harbinger for the decline of Golkar and the departure of Suharto from Indonesian politics. In the May 1997 legislative elections, Golkar managed to allegedly secure 74.3% of the popular vote, amid massive violence that killed over one hundred political activists. Violence continued after the elections and was worsened by the Asian economic crisis. After severe devaluation of the rupiah in August and October of 1997, Suharto accepted an International Monetary Fund (IMF) loan package but failed to carry out IMF-imposed conditions for economic reform. By December, news of Suharto's worsening physical health also cast doubt on his ability to see Indonesia through a worsening economic and political situation.
After Suharto won an unopposed presidential election in March 1998, student protests swept Jakarta and ethnic tensions also swelled as Chinese merchants were attacked. In East Timor, José Ramos-Horta urged the government to agree to a cease-fire and cooperation with the UN to determine the ultimate governance structure for the country. On 21 May 1998, Suharto resigned as president, after hundreds of people were killed, looting swept through the capital, and thousands of foreigners living or working in Indonesia were evacuated in months of unrest. B. J. Habibie, the former vice president, was sworn in as president. Upon assuming the presidency, he adopted a conciliatory posture toward defusing the East Timor crisis by stating that East Timor may be given "special status" with increased autonomy within Indonesia. In August 1998, Portugal and Indonesia met to discuss the future of the province. After significant pressure from the United Nations, Australia, and Portugal, Habibie agreed on 27 January 1999 to hold a referendum for the province. Despite widespread violence instigated by the pro-Indonesia armed militia, 98% of voters cast their ballots on 30 August, with 78.5% in favor of independence. This was followed by a rampage by pro-Indonesia forces who looted and burned the entire province creating a major humanitarian situation and refugee crisis. With the aid of Australian troops, the United Nations intervened with approximately 8,000 troops to restore order and establish humanitarian programs. Meanwhile, in Irian Jaya and Aceh, the military forces and the national police continued to commit extra-judicial killings in 2000.
B. J. Habibie's political fortunes waned in the aftermath of the UN-sponsored referendum in East Timor. His state of the nation address to the People's Consultative Assembly in October 1999 did not allay the perception that he had not exercised the appropriate leadership in handling domestic and international matters. Pressure on Habibie mounted and he subsequently resigned as a result of a no confidence vote. In 20 October elections in the People's Consultative Assembly, the first free elections in 44 years, Abdurrahman Wahid, the leader of the National Awakening Party and a near-blind Muslim cleric, was pitted against Megawati Sukarnoputri. Megawati's party won the most votes, but rather than negotiate with other politicians to form a coalition, Megawati allowed the more experienced Wahid to become president. Despite protest from her supporters, Megawati asked backers to refrain from violent protest. She became vice president. Wahid worked to curb the influence of the military and promised major reforms in the government.
In July 2001, Wahid declared a state of emergency and ordered parliament dissolved, after months of opposition from legislators over the competence of his administration. On 23 July 2001, legislators in the People's Consultative Assembly voted 591–0 to remove Wahid from the presidency. He had been charged with corruption and incompetence, being accused of embezzling US $4.1 million in state funds and illegally accepting US $2 million from the Sultan of Brunei. He was cleared of all charges that May, but the parliament continued to insist upon impeachment proceedings based on dissatisfaction with his administration. Megawati was sworn in as president immediately after Wahid's removal.
Megawati, a Muslim who is however identified with her nationalist-secular policies, faced demonstrations upon assuming office from strict Islamic fundamentalists calling for the establishment of Shari'ah law. She also had to face the Aceh independence movement, as more than 1,000 people were killed in the province in 2001, adding to the thousands more that had been killed in the past decade. Megawati expressed support for the United States-led war on terrorism following the 11 September 2001 terror attacks on the World Trade Center and the Pentagon, and she visited the United States the following week.
Following the fall of Suharto, Indonesia experienced a resurgence of Islamic activity. The main extremist Islamist organizations in Indonesia are Darul Islam, the Islamic Defender's Front and Laskar Jihad. Laskar Jihad is the most prominent and organized of Indonesia's radical Islamist organizations, and between 300–400 new members joined within the first month following the 11 September attacks. On 12 October 2002, Indonesia experienced its own terror attack. Two nightclubs in the resort town of Kuta on the island of Bali were bombed, killing over 190 people, the majority young Western tourists. Many of the casualties came from Australia. On 18 October, President Megawati issued an emergency decree to give the government expanded powers to fight terrorism. This act came after international criticism directed at her government for not taking the necessary steps to address the problem of terrorism. Megawati permitted the arrest of Abubakar Bashir, a Muslim cleric who is the spiritual leader of Jemaah Islamiyah. Jemaah Islamiyah was accused of staging the Bali bombings. It has links to the al-Qaeda organization.
Following its independence referendum held in August 1999, East Timor was governed by UNTAET (the United Nations' Transitional Administration in East Timor), and a National Consultative Council. A constituent assembly was elected in September 2001 with the task of writing a constitution for the country. In April 2002 José Alexandre "Xanana" Gusmão was elected president, and on 20 May 2002 East Timor became an independent nation.
In June 2000, 2,500 activists representing 250 tribal groups in Irian Jaya declared the region—which they call West Papua—a sovereign state. The region was granted limited autonomy by parliament in October 2001, but many inhabitants, including independence rebels, rejected the measure and called for full independence. On 9 December 2002, the government and the separatist Free Aceh Movement (GAM) signed a peace deal aimed at ending over three decades of violence. The accord provides for autonomy and free elections in Aceh; in return the GAM must disarm.
Demonstrators protested price increases on basic necessities such as fuel and electricity in January 2003, commodities that have been rooted in corruption. Megawati, originally seen as a friend of the poor, was urged to resign by some for failing to eliminate corruption. She will stand as a candidate for the 2004 presidential elections.