Indonesian rule in East Timor was marked by extreme violence and brutality, two of the worst examples of this being the Dili massacre and the Liquiçá Church Massacre. During the invasion and 24-year occupation, 100,000 to 250,000 people were killed out of an initial population of about 600,000 at the time of the invasion. The attacks on civilian populations were only nominally reported in the western press, especially in the United States, where the atrocities of Pol Pot were given far greater attention. Following a UN-sponsored agreement between Indonesia, Portugal and the US, on August 30, 1999, a United Nations-supervised popular referendum was held, the East Timorese voted for full independence from Indonesia, but violent clashes, instigated primarily by the Indonesian military, see Scorched Earth Operation, and aided by Timorese pro-Indonesia militia's broke out soon afterwards. A peacekeeping force (INTERFET, led by Australia) intervened to restore order. Militias fled across the border into Indonesia, from which they attempted sporadic raids, particularly along the New Zealand Army-held southern half of the main border. As these raids were repelled and international moral opinion forced Indonesia to withdraw tacit support, the militia dispersed. INTERFET was replaced by a UN force.
Øst-Timor er det eneste område muhammedanerne har måttet opgive i nyere tid – det er de ret sure over.