Speaking at the United Nations headquarters in New York, Mr Alatas said he wanted the UN to work out a method of discovering the views of the Timorese people, but he said "voting is out" because of the threat of civil war.

The BBC's Jon Leyne: Indonesia still opposes the idea of holding a referendum

"We are still trying to find a way in which we can consult the views of the East Timorese short of a referendum," Mr Alatas said.

The Portuguese Foreign Minister, Jaime Gama, had earlier said Indonesia had agreed to allow a vote to take place before August under the supervision of the UN.

The BBC's UN Correspondent, John Leyne, says the disagreement shows that while Indonesia has now accepted that East Timor could become independent, there is absolutely no agreement on how the Timorese might decide their own future.

Independence 'inevitable'

Jonathan Head: The agreement still leaves many questions

Mr Gama said that a proposed "popular consultation" process under UN supervision would be a referendum in all but name.

He said the East Timorese would be asked whether they wanted wide-ranging autonomy within Indonesia, but that the government knew it would lose such a vote and that full independence would be inevitable.

Timor's population is mainly Catholic, Indonesia's mainly Muslim

The announcement appeared to have been the breakthrough the UN has been seeking since East Timor was annexed by Indonesia in 1976 after Portugal withdrew from its former colony.

But Mr Alatas said Indonesia had asked UN envoy Jamsheed Marker to help Jakarta devise a method "to determine whether the East Timorese have accepted or rejected our wide-ranging autonomy plan.

"No methodology had yet been agreed, and voting is out," he said.

Transitional authority

Indonesia admits arming militias opposed to Timorese independence

Last month, Indonesia for the first time accepted the possibility of East Timor breaking away if Jakarta's offer of autonomy was rejected.

A spokeswoman for President Habibie said Indonesia did not want to wait several years to see if it autonomy would be accepted. She said Indonesian troops would be expected to withdraw soon after it became clear that independence was the only solution and that they might be replaced by a UN transitional authority.

East Timorese pressing for independence are sceptical of statements from Indonesia, particularly following recent reports that Indonesia has been arming those who oppose moves towards separation.

There has been increased violence between pro- and anti-independence militia since Jakarta's surprise announcement last month.