The UN started to prepare for the referendum by setting up the United Nations Assistance Mission for Timor-Leste, UNAMET. On June 3, 1999 the UN raised its flag on the soil of Timor-Leste. In September 1999 the people of Timor-Leste voted overwhelmingly – 78% – in favour of independence from Indonesia. The pro-integration militia gangs and the Indonesian armed forces responded with extraordinary brutality, rampaging and plundering across the country

As a result, one-third of the population were forced to resettle in refugee camps in West Timor and neighbouring islands. Another one-third looked for refuge in the mountains of Timor-Leste. Between 1,000 and 2,000 people are reported to have died in the violence. The UN Security Council authorized a multinational force (INTERFET) under the unified command structure of a member state, Australia, to restore peace and security. The UN also launched a large-scale humanitarian operation including food supplies and other basic services.

On October 25 1999, the UN Security Council established the United Nations Transitional Administration in Timor-Leste (UNTAET) as an integrated, multidimensional peacekeeping operation responsible for the administration of Timor-Leste during its transition to independence.