By Keith B. Richburg

Balibo, East Timor - Ignoring threats of militia violence and predictions of civil war, the East Timorese - many walking for miles and waiting for hours under a scorching sun - voted Monday on whether to remain a part of Indonesia with broad autonomy or become one of the world's newest and poorest nations. United Nations officials, who organized the referendum, estimated the turnout at more than 80 percent of some 439,000 registered voters, suggesting that the anti-independence militia's months-long campaign of intimidation was not enough to keep people away from the polls.

The voting was marred by the stabbing death of a Timorese UN worker at Ermera just after the polls closed. Other violence, including militia attacks, briefly closed down seven of the town's 200 polling stations. All reopened, and UN officials said no one was prevented from voting. The result is expected to be announced in a week, after it is reviewed and certified by the UN secretary-general, Kofi Annan.

But analysts said the high turnout - even in volatile western towns like this one considered a militia stronghold - suggested that the vote would be heavily for independence. ''One thing is manifestly clear,'' said Jamsheed Marker, the UN secretary-general's special representative for East Timor. ''Whatever the outcome of the ballot, today the eagle of liberty has spread its proud wings over the people of East Timor.'' "Many of the people who went to the polling stations today did so under conditions of considerable hardship,'' he added. ''They defied poverty, distance, climate, terrain, and in some cases dark intimidation in order to exercise their God-given right to vote in freedom.''

Xanana Gusmao, East Timor's likely first president if it becomes independent, was escorted from his prison house to a Jakarta polling place and allowed to vote absentee. Another prominent independence leader, the Nobel laureate Jose Ramos-Horta, also voted absentee in Australia since he is banned by the Indonesian government from traveling here.

The day was not trouble-free. The worst incident, in the town of Gleno, happened just after the U.S. ambassador, Stapleton Roy, had arrived with a small U.S. Embassy delegation to observe the voting. Several dozen members of the militia brandishing pistols burst into the polling station around noon, shouting that they would kill all election observers and accusing UN election workers of being biased in favor of independence. Several shots were fired inside and outside the polling place, and Mr. Roy was whisked away. At least two UN staffers were injured. The police, who were roundly praised for containing violence across the territory, repulsed the militia by firing into the air, witnesses said. It was at this site that the UN worker was later reported stabbed and killed.

Another lingering question was to what extent people may have been intimidating into voting against independence because of the heavy militia presence outside the polling places - particularly in distant towns like this one in the volatile western districts. At a polling place here, two Australian election observers said they arrived at about 10 A.M. - more than three-and-a-half hours after the polls opened - and found militiamen and armed police checking identity cards of the 3,000 or so voters waiting in line, in direct violation of election rules. When the observers arrived, the militiamen left. A few minutes later, the observers said, they saw two carloads of militiamen pass by the polling place, the first filming the voters in line with a hand-held camera and the second taking photographs from the car window. Not far away from the polling site, Indonesian police were busy loading hundreds of people into the back of two large yellow trucks. They explained that these were refugees from East Timor who had fled to Indonesia after the 1975 invasion and were returning to vote, which is allowed under UN rules. The people on the truck said they had all voted against independence. But the Australian observers said they witnessed money being passed to the refugees. At another western polling station, at Bobanaro, a UN election worker said he complained to the police about militiamen - recognizable despite their civilian clothes - milling around outside the site. ''We had some militia chiefs hanging around,'' he said. ''We asked the police to move them. They go, they come back, they go, they come back.''

What will be the reaction now of the army-backed militia groups responsible for the terror of the last several months? Many observers had expected the militias to stage major attacks on polling day to disrupt the ballot or have it canceled outright, but instead the voting proceeded relatively smoothly. UN officials said no Timorese were prevented from voting. Now the fear is that the pro-Indonesian militias will refuse to accept the result if, as appears likely, it is for independence.

One likely strategy, according to UN officials and diplomats, is that the militias may retreat to their stronghold in the west around Maliana and here at Balibo, and reject the vote, effectively partitioning tiny Timor. "It could be the partition strategy - just fortify yourself in Maliana and say come and get us,'' said a Western diplomat. ''The Indonesians could just covertly help them from across the border.'' To guard against this, UN officials said all of the ballots will be mixed before they are counted so no district will be able to tell separately how its residents voted. All the ballots are being taken to the capital, Dili, by helicopter, for counting. One flamboyant militia leader, Eurico Guterres, raised the possibility of more strife when he warned that he planned to blockade East Timor's roads and its airport to prevent the territory's ''political elite'' from fleeing if violence erupts. Mr. Guterres has repeatedly warned of civil war if the territory opted for independence over autonomy. Asked if his threats should be taken seriously, a diplomat said: ''It depends on the military. If they pull the plug on Eurico and the others, then this could all be over with.''

There were some sins in recent days of a more conciliatory attitude from officials in Jakarta, who, after weeks of covert support for the militia terror campaign, may now be resigned to seeing the territory break free. The fear among Indonesian officials, particularly within the powerful military, is that allowing East Timor to separate might prompt secessionist movements elsewhere such as Aceh Province or Irian Jaya. But lately, the military commander here has been replaced, President B.J. Habibie of Indonesia on Sunday gave a speech pledging to respect the result of the vote, and, also on Sunday, Mr. Guterres committed the militia to a plan to ban the carrying of weapons in public. This commitment may have come from heavy pressure. In another possible sign of a policy swing, the Indonesian police Monday appeared to be effectively enforcing security around the polling stations after weeks of criticism for inaction.