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.