United Nations, New York - Secretary-General Kofi Annan has decided that voter registration can go ahead in East Timor, and Portuguese and Indonesian senior officials were meeting Thursday at the United Nations to discuss arrangements for the vote on the territory's future.

In a letter on Wednesday to the Security Council, Mr. Annan said that voter registration would begin Friday, three days later than originally scheduled, after receiving ''positive assurances'' from Indonesian authorities about security conditions. He left open the possibility of scrapping or delaying the poll depending on Indonesian cooperation in ensuring ''meaningful, visible improvements'' in the security situation.

Mr. Annan wants to ensure that the pro-Indonesian militia no longer operate with impunity in the former Portuguese colony where it has been intimidating voters and harassing UN personnel. The ballot, in which the East Timorese are to decide whether their territory should remain part of Indonesia or move toward independence, is currently scheduled for Aug. 21 or 22. Mr. Annan has already delayed the timing of the vote itself by two weeks because of the militia violence.

On Wednesday, he told the Security Council that despite Indonesian promises of cooperation, he was not able to conclude at present that the necessary security conditions existed for the ballot next month to go ahead. As a result, half-way through the 20-day registration period, he would ''determine whether there had been enough significant progress to continue registration'' so that the East Timorese could vote ''safely and free of intimidation.''