Rival militia leaders: All smiles on the eve of the poll
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In the latest incidents, two militiamen were killed in an area of the capital, Dili, controlled by pro-independence rivals.
The UN special envoy to East Timor, Jamsheed Marker, has expressed optimism over the turnout in Monday's referendum after rival militias agreed not to disrupt voting.
Voting is due to take place between 0630 and 1600 local time (2230-0800 GMT).
Arriving to observe the ballot in person, Mr Marker said he felt "very positive", and described the joint disarmament pledge by the rival armed camps as "very encouraging".
Mr Marker said he had also received security "assurances" from Indonesian Foreign Minister, Ali Alatas.
Indonesian President BJ Habibie made a last-minute appeal for East Timorese not to vote for independence.
"I call on all to remain united in building a more prosperous future together with their brothers and sisters," he said, pledging that the Indonesian security forces would police the "popular consultation" responsibly.
'Historic' agreement
Commanders from the pro-independence rebel movement Falantil and leaders of militias opposed to cutting ties with Indonesia met on Sunday at the UN's headquarters in Dili to announce their accord.
At a press conference attended by Indonesian police and military, they pledged to keep their forces in designated areas and to accept the results of the ballot.
Eurico Guterres, commander of one of the pro-Indonesian militias, Aitarak, described the agreement as "historic", while Falantil leader Falur Rate Laek said it paved the way for a peaceful vote.
"We wanted this agreement so that the people in the mountains can come down and vote tomorrow," he said.
A BBC correspondent in Dili says the UN is determined to ensure the vote goes ahead - but he says there are still uncertainties about the sincerity of the factions and whether the leaders can control their forces.
Violence continues
The run-up to the referendum has been marred by serious violence, most of it blamed on the pro-Jakarta militias, and has brought world condemnation on Indonesia.
Ten houses were reported burned, and a number of people injured, in a militia attack in the western Oecussi enclave overnight.
At least 12 people have died in the last week, and hundreds have been killed during campaigning for the referendum.
Pro-Jakarta militias have roamed unchecked through the territory, threatening to kill those who vote for independence. Many people have fled them in terror.
Many international observers have expressed concern that the violence would prevent many of East Timor's 450,000 registered voters from taking part in the referendum which will offer them the choice between wide-ranging autonomy within Indonesia or independence.
The Nobel Prize-winning Bishop of Dili, Carlos Felipe Ximenes Belo, called on Sunday for voters to turn out despite any intimidation they might face.
"Vote according your conscience. At this time I ask all of you not to be afraid. Be brave and choose the future of East Timor," he said. Bishop Belo is the head of the Roman Catholic Church in the province.
The ballot is widely predicted to go in favour of independence which would end more than 23 years of Indonesian occupation in the former Portuguese colony.