The 1999 East Timorese crisis began with attacks by pro-Indonesia militia groups on civilians, and expanded to general violence throughout the country, centred in the capital Dili. The violence intensified after a majority of eligible East Timorese voters chose independence from Indonesia. Some 1,400 civilians are believed to have died. A UN-authorized force (INTERFET) consisting mainly of Australian Defence Force personnel was deployed to East Timor to establish and maintain peace.
Background
Independence for East Timor, or even limited regional autonomy, was not allowable under Suharto's New Order. Notwithstanding Indonesian public opinion in the 1990s occasionally showing begrudging appreciation of the Timorese position, it was widely feared that an independent East Timor would destabilise Indonesian unity. Renewed United Nations-brokered mediation efforts between Indonesia and Portugal began in early 1997. The 1997 Asian Financial Crisis, however, caused tremendous upheaval in Indonesia and led to Suharto's resignation in May 1998, ending his thirty-year presidency. Prabowo, by then in command of the powerful Indonesian Strategic Reserve, went into exile in Jordan and military operations in East Timor were costing the bankrupt Indonesian government a million dollars a day. The subsequent "reformasi" period of relative political openness and transition, included unprecedented debate about Indonesia's relationship with East Timor. For the remainder of 1998, discussion forums took place throughout Dili working towards a referendum. Indonesian Foreign Minister Alatas described plans for phased autonomy leading to possible independence as "all pain, no gain" for Indonesia. On 8 June 1998, three weeks after taking office, Habibie, as Suharto's successor, announced that Indonesia would soon offer East Timor a special plan for autonomy.
In late 1998, the Australian Government of John Howard drafted a letter to Indonesia advising of a change in Australian policy, and advocating a referendum on independence within a decade. President Habibie saw such an arrangement as implying "colonial rule" by Indonesia and he decided to call a snap referendum on the issue.
Indonesia and Portugal announced on 5 May 1999 that a vote would be held allowing the people of East Timor to choose between the autonomy plan or independence. The vote, to be administered by the United Nations Mission in East Timor (UNAMET), was originally scheduled for 8 August but later postponed until 30 August. Indonesia also took responsibility for security; this arrangement caused worry in East Timor, but many observers believe that Indonesia would have refused to allow foreign peacekeepers during the vote.
Voting and violence
As groups supporting autonomy and independence began campaigning, a series of pro-integration paramilitary groups of East Timorese began threatening and committing violence around the country. Alleging pro-independence bias on the part of UNAMET, the groups were seen working with and receiving training from Indonesian soldiers. Before the May agreement was announced, an April paramilitary attack in Liquiça left dozens of East Timorese dead. On 16 May 1999, a gang accompanied by Indonesian troops attacked suspected independence activists in the village of Atara; in June another group attacked a UNAMET office in Maliana. Indonesian authorities claimed to be helpless to stop what it claimed was violence between rival East Timorese factions, but Ramos-Horta joined many others in scoffing at such notions. In February 1999 he said: "Before [Indonesia] withdraws it wants to wreak major havoc and destabilization, as it has always promised. We have consistently heard that over the years from the Indonesian military in Timor."
As militia leaders warned of a "bloodbath", Indonesian "roving ambassador" Francisco Lopes da Cruz declared: "If people reject autonomy there is the possibility blood will flow in East Timor." One paramilitary leader announced that a "sea of fire" would result in the event of a vote for independence. As the date of the vote drew near, reports of anti-independence violence continued to accumulate.
The day of the vote, 30 August 1999, was generally calm and orderly. 98.6 per cent of registered voters cast ballots, and on 4 September UN Secretary-General Kofi Annan announced that 78.5 per cent of the votes had been cast for independence. Brought up on the "New Order"'s insistence that the East Timorese supported integration, Indonesians were either shocked or incredulous that the East Timorese had voted against being part of Indonesia. Many accepted media stories blaming the supervising United Nations and Australia who had pressured Habibie for a resolution.