Joanna Jolly and Agencies in Dili – Anarchy returned to East Timor's capital yesterday with at least five people killed as hundreds of anti-independence militiamen targeted the United Nations. The violence came as the counting of votes from the autonomy referendum began.

Rampaging militiamen shot and hacked a teenager to death with machetes outside the UN compound in Dili – the most brazen violence since the historic referendum on Monday.

A nurse at a Catholic clinic identified the man who died as Jorges Fransisco Bonaparte, 19. He was shot through the neck and had several deep cuts and bruises, and was pronounced dead at the clinic.

Dili's streets were deserted last night and up to 1,000 residents were sheltering in the UN compound.

Witnesses said at least five East Timorese were believed killed and many people – including several foreign journalists – wounded. They said the final death toll could be much higher. Fires were seen across Dili and the home of a UN translator was burned down.

Indonesian riot police sent in an hour after the violence erupted fired volleys of warning shots and dispersed the attackers. They claimed order had been restored and the offices of the UN Mission in East Timor were safe, but observers described Dili as "under militia control".

"We can't protect these people," said one UN staff member, referring to those seeking safety at the compound. "There will be a backlash against the UN now that our vulnerability has been exposed."

The UN Security Council last night began an emergency session to discuss the violence.

In a statement, UN Secretary General Kofi Annan called on Indonesian police "to arrest those responsible for the violence and to take immediate steps to ensure it does not happen again".

Indonesia's military commander in East Timor, Colonel Mohammad Muis, said his forces were on full alert. At least 75 riot police were reportedly fanning out to clear the area. Police in Jakarta said 360 officers from an elite unit would be flown in today.

The referendum is expected to favour independence from Indonesia for the territory, which was invaded in 1975, triggering years of guerilla warfare and human rights abuses in the former Portuguese colony.

The attack yesterday was the most serious on the UN since it took over organisation of the vote last May. One UN worker was killed on Monday and two were feared dead in attacks.

The fighting between militias armed with shotguns and independence supporters carrying knives and Molotov cocktails was initially not directed at the UN.

Members of the Aitarak militia then fired shots into a group of independence supporters and the shooting moved towards the compound. During the attack, an Indonesian military truck was seen to drive through the militia, then turn round and leave. A group of Indonesian police was also seen driving near the fighting without intervening.

UN staff radioed the police, who said their arrival was delayed because they did not know the way to the compound, used by the UN since June.