Ignoring threats of militia violence and predictions of civil war, hundreds of thousands of East Timorese walked for miles and waited for hours Monday to vote for the first time on whether to remain a part of Indonesia with broad autonomy, or become one of the world's newest--and poorest--nations.

Early this morning, United Nations officials, who organized the referendum, estimated the turnout at 98.6 percent of the 439,000 registered voters, suggesting that the anti-independence militia's months-long campaign of terror and intimidation was not enough to keep people away from the polls.

The voting was marred by the stabbing death of a Timorese U.N. worker at Ermera just after the polls closed. Other violence, including militia attacks, briefly closed seven of the 200 polling stations in East Timor, but U.N. officials said no one was prevented from voting, and all the stations reopened.

The result is expected to be announced in a week, after it is reviewed and certified by U.N. Secretary General Kofi Annan. But analysts said the high turnout across the territory of 800,000 people--even in volatile western towns like this one, which is considered a militia stronghold and a bastion of pro-Indonesian sentiment--suggested that the vote would be heavily for independence.

Concern for security remained high as militia leaders, who enjoy backing from elements in the Indonesian army, continued their threats against the prospect of independence and created an intimidating presence at some polling stations. Election observers cited apparent instances of voter bribery by the militias.

"One thing is manifestly clear," said Jamsheed Marker, the 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," Marker said at a news conference Monday in the capital, Dili. "They defied poverty, distance, climate, terrain and in some cases dark intimidation in order to exercise their God-given right to vote in freedom."

Independence fighter Xanana Gusmao, East Timor's likely first president if it becomes independent, was escorted from house arrest to a polling place in the Indonesian capital Jakarta and allowed to cast an absentee ballot. Another prominent independence leader, Nobel Peace Prize laureate Jose Ramos-Horta, also voted absentee in Sydney, Australia, because he is banned by the Indonesian government from traveling to his homeland.

Monday was not trouble-free. One of the worst incidents occurred in the town of Gleno, near Ermera, just after U.S. Ambassador Stapleton Roy arrived with a small delegation to observe the voting. Several dozen plainclothes militiamen brandishing pistols burst into the polling station just after noon, shouting that they would kill all election observers and accusing U.N. election workers of being biased in favor of independence.

Several shots were fired inside and outside the polling place, and Roy was whisked away. At least two U.N. staffers were injured in that attack. Police, who were praised on Monday for containing violence across the territory, repulsed the militiamen by firing into the air, witnesses said.

It was a member of the U.N. team supervising the ballot at this site, Joel Lopez Gomes, who was later reported stabbed and killed by a mob while on his way home. At U.N. headquarters, Annan voiced his "great dismay and sorrow" at "this deplorable act of violence."

A lingering question was to what extent people might have been intimidated into voting against independence because of the heavy militia presence outside polling places--particularly in remote towns like this one.

At a polling place in Balibo, two Australian election observers said they arrived at about 10 a.m.--more than 3 1/2 hours after the polls opened--and found militiamen and armed police checking the identity cards of the 3,000 or so voters waiting in line, in violation of election rules. After the observers arrived, the militiamen left.

A few minutes later, observers said, they saw two carloads of militiamen pass by the polling place, one filming the voters in line with a hand-held camera, and another taking photographs.

Not far from the polling site, Indonesian police were busy loading hundreds of people into the back of two large yellow trucks. The police said they were refugees from East Timor who had fled to Indonesia after the 1975 invasion and were returning to vote, which is allowed under U.N. rules. The people on the truck said they had all voted against independence. But the Australian observers said they saw money being passed to the refugees--50,000 to 100,000 Indonesian rupiah each, the equivalent of $6 to $13.

A key unanswered question after Monday's vote concerns the reaction of the army-backed militia groups responsible for the violence and terror of the last several months, in which dozens of people have died and more than 60,000 have been displaced.

The fear is that the pro-Indonesian militias will refuse to accept the result if it is for independence instead of autonomy. One likely strategy, according to U.N. officials and diplomats, is that the militias might retreat to their stronghold in the west, around Maliana and here at Balibo, and declare that they are rejecting the result, effectively partitioning tiny East 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" in West Timor, part of Indonesia.

One militia leader, Eurico Guterres, raised the possibility of more strife here 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. Guterres has repeatedly warned of civil war if the territory opts for independence.

CAPTION: Waiting to cast ballots, residents of the village of Hatukusi hold voting registration papers above their heads.

CAPTION: Xanana Gusmao, going to vote absentee in Jakarta, is expected to be president if independence wins.

CAPTION: East Timorese women wait to vote in Liquica, a village near the capital of Dili.