Even with the diverse security agreements, established to ensure that the Indonesian Army (TNI) would protect the organization of the ballot and to constrain the activities of militias, violent episodes took place in East Timor during the months leading to the consultation. Locations and members of the pro-independence National Council of Timorese Resistance (CNRT) were the main victims, although civilian East Timorese and U.N. personnel and equipment were also affected.

The first violent event after the consultation took place hours after the polling stations were closed, when a UNAMET worker was killed. However, when the result of the popular consultation, which rejected the special autonomy status and demanded independence for East Timor, was announced on the night of September 4, massive violence erupted. TNI factions or militias sponsored by it were largely identified responsible for this violence.

By the end of September 27, 1999, almost one month after the ballot and the beginning of the massacre, the United Nations established a Commission of Inquiry on East Timor to investigate human rights violations and other abuses. Its final report, which provides an overview of the post-ballot conflict, can be viewed below. The U.N. Security Council kept a close eye on the conflict. Here are the several resolutions it emitted in relation to the post-consultation violence in East Timor. 

James Dunn, former observer for UNAMET during the ballot, was commissioned by East Timor General Prosecutor Mohamed Othman to write an analysis on the causes, the development and consequences of the post-consultation violence.

Human Rights Watch produced a series of reports documenting the pre-consultation mounting tensions caused by the presence of unauthorized armed groups throughout the territory and the havoc they produced. After the vote was carried out, Human Rights Watched urged the international community to act before the widespread killing, while maintaining a close eye on the developments on East Timor.

The Carter Center prepared several statements noticing the increasing challenges to the security environment of the consultation. These declarations continued after the ballot, detailing the series of attacks and the evolution of the armed groups that perpetrated them.

The International Crisis Group elaborated materials on the persistence of several problems caused by the conflict years after it started and was controlled. Some of these topics include border security, challenges to the professionalization of security forces, and the situation of refugees. 

United Nations

Report of the International Commission of Inquiry on East Timor (January 31, 2000)

Security Council Post-Consultation Resolutions

UN SC Resolution 1264 (1999)

UN SC Resolution 1272 (1999)

UN SC Resolution 1319 (2000)

UN SC Resolution 1338 (2001)

UN SC Resolution 1392 (2002)

UN SC Resolution 1410 (2002)

UN SC Resolution 1473 (2003)

UN SC Resolution 1480 (2003)

UN SC Resolution 1543 (2004)

UN SC Resolution 1573 (2004)

UN SC Resolution 1599 (2005)

UN SC Resolution 1677 (2006)

UN SC Resolution 1690 (2006)

UN SC Resolution 1703 (2006)

UN SC Resolution 1704 (2006)

UN SC Resolution 1745 (2007)

UN SC Resolution 1802 (2008)

UN SC Resolution 1867 (2009)

UN SC Resolution 1912 (2010)

UN SC Resolution 1969 (2011)

UN SC Resolution 2037 (2012) 

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East Timor General Prosecutor Commission

James Dunn, Crimes Against Humanity in East Timor (February 14, 2001)

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Human Rights Watch

Indonesia. The violence in Ambon (March 1, 1999)

Joint demarche needed on East Timor militias (April 8, 1999)

Stop bank loans until militias disarmed (April 20, 1999)

Backgrounder – The Indonesian Army and civil militias in East Timor (April 24, 1999)

Donors must register more forceful protest (July 1, 1999)

Stop militia violence (July 7, 1999)

More deaths inevitable in East Timor unless donor act (August 27, 1999)

Suspend aid until militias brought under control (September 1, 1999)

Indonesian government must prevent East Timor bloodbath (September 3, 1999)

The world must act or be complicit in the killing (September 5, 1999)

Martial law will make things worse (September 7, 1999)

Refugee camps in West Timor offer no refuge (September 10, 1999)

Habibie decision welcome, but what are the terms? (September 12, 1999)

Protection for displaced persons in East and West Timor (September 13, 1999)

HRW urges adoption of UN Security Council Resolution on East Timor (September 14, 1999)

Stop transmigration (September 20, 1999)

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The Carter Center

Pre-Consultation Statements

Statement on East Timor Elections, July 17, 1999

Statement on East Timor Elections, July 25, 1999

Statement on East Timor Elections, August 1, 1999

Statement on East Timor Elections, August 8, 1999

Statement on East Timor Elections, August 16, 1999

Statement on East Timor Elections, August 22, 1999

 Post-Consultation Statements

Statement on East Timor Elections, September 1, 1999

Statement on East Timor Elections, September 13, 1999

Statement on East Timor Elections, September 22, 1999

International Crisis Group

Managing tensions on East Timor-Indonesia border (May 6, 2006)

Security sector reform (January 17, 2008)

Displacement crisis (March 31, 2008)

No time for complacency (February 9, 2009)

Handing back responsibility to East Timor police (December 3, 2009)

Time for the UN to step back (December 15, 2010)

Return and reconciliation from Indonesia (April 18, 2011)

Veterans – An unfinished struggle (November 18, 2011)

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