The former Australian deputy prime minister Tim Fischer, who is observing the ballot, said reliable sources had told him that two missing United Nations employees were probably dead after an incident late on Monday in Atsabe town in which another member of staff is known to have died.
Some 150 UN workers were trapped all day in Gleno, in Ermera district, south of the capital, Dili, after militiamen opposed to East Timorese independence rampaged through the town and blocked roads to the capital.
A convoy of 17 cars was finally allowed to leave during the night, after UN officials flew in by helicopter to negotiate with the gunmen.
There were widespread reports of harassment in the western parts of the territory and at Dili's airport and waterfront militiamen tried to prevent travellers leaving East Timor.
The scale of voting in Monday's referendum far exceeded even the most optimistic forecasts. Of 438,500 voters registered in East Timor, 432,300 voted, a turn-out of 98.6 per cent. "The massive voter turn-out is proof, absolute proof, that the campaign of intimidation, violence and threats that attempted to destabilise this popular consultation was a complete failure," said David Wimhurst, spokesman of the UN Assistance Mission to East Timor (Unamet). "It could not work, it did not work, and it will not work.
"Knowing this to be true, it is imperative that everybody lay down their arms, cease all violent activity and instead focus their energies on the long process of reconciliation," he said.
But with several days to go before the announcement of the final result, it is clear reconciliation is still a long way off between the pro-independence and pro-Indonesian sides.
All day black-clad members of the Aitarak (Thorn) militia were visible in Dili, preventing small boats from leaving the waterside. Witnesses said that they smashed windows in the headquarters of the National Council for Timorese Resistance, a pro-independence organisation, which had been evacuated after a similar attack last Thursday.
Anti-independence forces appeared to be preparing themselves for a defeat by raising questions about the legitimacy of the vote.
The United Front, the main pro-Jakarta umbrella group, dismissed Monday's vote as "garbage", accusing Unamet of bias.
"Most of the pro-integration supporters have come to the conclusion that Unamet is really encouraging and backing the people of East Timor to break East Timor away from Indonesia," the group said in a statement signed by the spokesman Basilio Araujo.
"What outcome will one expect from all this garbage? Only God knows, but one thing is for sure, in computing terms it says: `Garbage in, garbage out'."
In Ermera a ballot-box spilt open as it was being loaded on to a helicopter under a hail of gunfire and stones thrown by militiamen, although only two ballot papers were lost. UN investigators flew to Atsabe yesterday to investigate the first UN casualty, a 49-year-old East Timorese election worker who was stabbed to death on Monday evening.
The relative peacefulness of Monday's poll gave rise to hopes that the Indonesian security forces had abandoned their policy of supporting the militias, but yesterday they appeared to have resumed their policy of turning a blind eye to militia activity.
In an incident at the main airport, East Timorese travellers were prevented by militiamen from boarding their flight to Jakarta, as policemen looked on.