[7] The overthrow of the popular and short-lived Fretilin-led government sparked a violent quarter-century occupation in which approximately 100,000–180,000 soldiers and civilians are estimated to have been killed or starved to death.

[6] The Commission for Reception, Truth and Reconciliation in East Timor documented a minimum estimate of 102,000 deaths as a result of the conflict in East Timor during the period 1974 to 1999, as well as a large part of the consequences of Indonesian war crimes during the invasion of Dili, including 18,600 violent killings and 84,200 deaths from disease and starvation; Indonesian forces and their auxiliaries combined were responsible for 70% of the killings.

[13] Colonial rule was replaced by the Japanese during World War II, whose occupation spawned a resistance movement that resulted in the deaths of 60,000 people, 13 percent of the population at the time.

[14] In April 1974, the left-wing Movimento das Forças Armadas (Armed Forces Movement, MFA) within the Portuguese military mounted a coup d'état against the right-wing authoritarian Estado Novo government in Lisbon (the so-called "Carnation Revolution"), and announced its intention rapidly to withdraw from Portugal's colonial possessions (including Angola, Mozambique and Guinea, where pro-independence guerrilla movements had been fighting since the 1960s).

[17] Meanwhile, Fretilin (the Revolutionary Front of Independent East Timor) was composed of administrators, teachers, and other "newly recruited members of the urban elites.

[20] By April 1975, internal conflicts split the UDT leadership, with Lopes da Cruz leading a faction that wanted to abandon Fretilin.

[22] UDT's violent takeover thus provoked the three-week long civil war, in pitting its 1,500 troops against the 2,000 regular forces now led by Fretilin commanders.

[23] Indonesian nationalist and military hardliners, particularly leaders of the intelligence agency Kopkamtib and special operations unit, Opsus, saw the Portuguese coup as an opportunity for East Timor's annexation by Indonesia.

[25] Indonesian domestic political factors in the mid-1970s were not conducive to such expansionist intentions; the 1974–75 financial scandal surrounding petroleum producer Pertamina meant that Indonesia had to be cautious not to alarm critical foreign donors and bankers.

These concerns were successfully used to garner support from Western countries keen to maintain good relations with Indonesia, particularly the United States, which at the time was completing its withdrawal from Indochina.

[29] John Taylor writes that Indonesia invaded for three main reasons: (1) to avoid the “negative example” of an independent province, (2) to have access to the high initial estimates of oil and natural gas under the Timor Sea (initial estimates which turned out to be largely mistaken), and (3) following the fall of South Vietnam, to become Southeast Asia's major military partner of the United States.

"[43] In one incident, a group of fifty men, women, and children – including Australian freelance reporter Roger East – were lined up on a cliff outside of Dili and shot, their bodies falling into the sea.

[46] Though the Indonesian military advanced into East Timor, most of the populations left the invaded towns and villages in coastal areas for the mountainous interior.

[48] The military continued to restrict all foreigners and West Timorese from entering East Timor, and Suharto admitted in August 1976 that Fretilin "still possessed some strength here and there.

"[49] By April 1977, the Indonesian military faced a stalemate: Troops had not made ground advances for more than six months, and the invasion had attracted increasing adverse international publicity.

[50] In the early months of 1977, the Indonesian navy ordered missile-firing patrol-boats from the United States, Australia, the Netherlands, South Korea, and Taiwan, as well as submarines from West Germany.

Attempts by the United Nations Secretary General's Special Representative, Vittorio Winspeare Guicciardi to visit Fretilin-held areas from Darwin, Australia were obstructed by the Indonesian military, which blockaded East Timor.

On 31 May 1976, a 'People's Assembly' in Dili, selected by Indonesian intelligence, unanimously endorsed an 'Act of Integration', and on 17 July, East Timor officially became the 27th province of the Republic of Indonesia.

The occupation of East Timor remained a public issue in many nations, Portugal in particular, and the UN never recognised either the regime installed by the Indonesians or the subsequent annexation.

[71] The island's original division into east and west, Indonesia argued after the invasion, was "the result of colonial oppression" enforced by the Portuguese and Dutch imperial powers.

Previously secret files of the Australian Department of Foreign Affairs and Trade, released in September 2000, showed that comments by the Whitlam Labor party government may have encouraged the Suharto regime to invade East Timor.

[citation needed] These files from the Department of Foreign Affairs and Trade also outlined Australian National Security motivations for a Portuguese independent Timor.

Repeatedly mentioned in these files are Australian oil interests in Timorese waters; as well as the potential for a renegotiation of the Portuguese Timor sea border North of Australia.

The fall of Suharto and a shift in Australian policy by the Howard government in 1998 helped precipitate a proposal for a referendum on the question of independence for East Timor.

[84] A week after the invasion of East Timor the National Security Council prepared a detailed analysis of the Indonesian military units involved and the US equipment they used.

[91] While the US government claimed to have suspended new arms sales to Indonesia from December 1975 to June 1976, military equipment already in the pipeline continued to flow,[89] and the US made four new offers of arms during that six-month period, including supplies and parts for 16 OV-10 Broncos,[89] which, according to Cornell University Professor Benedict Anderson, are "specially designed for counter-insurgency actions against adversaries without effective anti-aircraft weapons and wholly useless for defending Indonesia against a foreign enemy."

"[94] The CAVR stated in the "Responsibility" chapter of its final report that US "political and military support were fundamental to the Indonesian invasion and occupation" of East Timor between 1975 and 1999.

"[95][96] Clinton Administration officials told the New York Times that US support for Suharto was "driven by a potent mix of power politics and emerging markets."

The covert military assistance provided, which most of it went straight into East Timor and was used against non-combatants, by the Ford administration to Suharto's regime in Indonesia was kept hidden from Congress and the public.

[98] On 12 December 1975, the United Nations General Assembly adopted a resolution that "strongly deplored" Indonesia's invasion of East Timor, demanded that Jakarta withdraw troops "without delay" and allow the inhabitants of the island to exercise their right to self-determination.