The Popular Consultation took place on August 30, 1999. 451,792 people had registered to vote, of which 98.6 percent exercised their rights. When UN and Timorese poll workers arrived at 4:00 a.m. at the 200 polling centers throughout the territory they already found people waiting to vote. Voting began at 6:30 a.m., and there were reports that by 2:00 p.m. many voting centers had all their registered voters already casting their ballots. The last polling station closed at 6:30 p.m.
Ballots were moved that night to the counting center. On August 31 the scrutiny began in Dili, the capital of East Timor. Complaints of irregularities (mostly pressed by the United Front for East Timor Autonomy, an anti-independence group) were heard by electoral authorities on September 2 and 3. However, there was no sound proof of misbehavior, and complaints were dismissed.
UN Secretary-General Kofi Annan announced the final result of the vote on September 4 in New York City to the UN Security Council. Immediately after, the same consultation results were read in Dili showing 78.5 percent of electors had selected the preference favoring independence (rejecting special autonomy) and 21.5 selected the preference against independence (favoring special autonomy).