BBC Newsnight's Mark Urban: East Timor's freedom is not a foregone conclusion

Earlier on Tuesday a group of about 150 United Nations staff and international observers were besieged in the town of Gleno by heavily armed militiamen who went on the rampage destroying several homes.

After six hours the group was allowed to return to UN headquarters in Dili in a convoy of 17 vehicles.

BBC News' Matt Frei: UN observers have no real protection in "a lawless place"

Elsewhere the UN operation in East Timor (Unamet) says two local members of staff are missing following a similar stand-off in the nearby town of Atsabe.

On Monday evening a local UN official was stabbed to death in Atsabe - the first and so far only confirmed casualty suffered by Unamet.

Buildings set ablaze

In Dili black-shirted militiamen set a number of buildings on fire and briefly seized control of the airport where they harassed passengers seeking to board the one daily scheduled flight out of the territory.

Eurico Guterres, the leader of the main Aitarak (Thorn) militia, said pro-independence students and members of the political elite would not be allowed to leave East Timor.

And in the town of Hera, 16km (10 miles) south of Dili, hundreds of militiamen armed with machetes and home-made guns were reported to be roaming the streets searching for pro-independence activists.

The BBC's Jonathan Head: "The turnout was astonishing"

"Don't try to come in here," one militia member told journalists. "It is very dangerous."

In spite of the renewed violence, Unamet says it has managed to transport all the blue plastic ballot boxes back to Dili where the counting process is due to begin on Wednesday.

Habibie welcomes ballot

Counting of votes begins on Wednesday

The poll achieved a massive 98.6% turnout and is thought to have produced a decisive vote in favour of breaking away from Indonesia.

In Jakarta, Indonesian President BJ Habibie welcomed the ballot as "very good, peaceful and fair".

"The most important thing is that we have to honour the decision of the East Timorese people," Mr Habibie said.

His comments echo those of Foreign Minister Ali Alatas who said Indonesia would hand over interim administration of East Timor to the United Nations, if results do favour independence.

Militias allege bias

However the United Front for East Timor Autonomy, an umbrella group of pro-Indonesian militias have denounced the referendum as "garbage" saying it would fuel fresh violence in the territory.

In a statement released on Tuesday the front said it was withdrawing co-operation with the UN until its concerns about alleged bias were addressed.

A 25-member reconciliation commission made up of representatives from pro- and anti-independence groups had been scheduled to convene its first meeting in East Timor on Thursday under the auspices of Unamet. But the militias' withdrawal caused the meeting to collapse.

Meanwhile the renewed violence and intimidation has once again forced to Unamet to appeal for calm.

No end in sight

Fear has already forced hundreds to flee their homes

"The people have expressed themselves massively," said spokesman David Wimhurst. "It is imperative that everybody lays down their arms and ceases all violent activity as it is completely futile."

The official result is expected within a week and will be announced simultaneously in New York and Dili. But whatever the verdict it will not bring an end to East Timor's problems.

Further militia attacks have demonstrated that what little law and order there was has broken down.

The BBC's Jonathan Head, who is in Dili, says those groups opposed to independence are being allowed to terrorise the population with impunity whilst the Indonesian police do nothing to stop them.