Jane Perlez, Jakarta – An Indonesian human rights court today acquitted six military and police officials of crimes against humanity in East Timor after a pro-independence vote three years ago, a verdict that did not please the Bush administration as it seeks to rebuild military ties here.

Five of the accused were on trial for failing to stop a massacre at the Ave Maria Church in Suai, in which at least 27 people, including three priests, were slain. The massacre was documented afterward as the most cold-blooded killing of the violence that consumed the territory after a vote for independence in September 1999.

Among those acquitted was the former regional police commander, Brig. Gen. Timbul Silaen, who was responsible for the security of the balloting, which was sponsored by the United Nations.

Anxious to renew its relationship with the police and military of Indonesia, the world's largest Muslim country, the Bush administration announced new aid for the police this month that American officials said was intended to help build a counter-terrorism unit.

Washington also said it would permit Indonesian Army officers to go to the United States for limited training, but underscored that a more robust training program would take place if the military demonstrated some accountability for what happened in East Timor. Today's verdicts were a "disappointment," an American official said. At a time when the United States is trying to "reach out" to Indonesia, the official said, the court's decision will not be helpful.

American officials had expressed some confidence that the government would live up to reassurances they said were given in private that Indonesia would do the "right thing" in the trials. But Indonesia has been intent on not appearing to allow any interference with its sovereignty, and President Megawati Sukarnoputri has been careful to steer a fairly neutral foreign policy.

Four of the six defendants today were officers of the Indonesian Army, which has regained some of its lost stature during the yearlong presidency of Mrs. Megawati.

The Bush administration has managed to overcome much of the resistance in Congress to renewing military ties with Indonesia. American military aid was severed by the Clinton administration after the East Timor bloodletting.

Today's verdicts could slow what the administration hoped would be a fairly smooth course to the resumption of healthy military relations.

The commander of United States forces in the Pacific, Adm. Thomas Fargo, who was in Jakarta today, suggested the need for the Indonesian military to face up to the past. Speaking just before the verdicts were announced, the admiral said, "It would be inappropriate for me to comment on the legal proceedings, but obviously a large part of our effort is to encourage accountability and reform."

On Wednesday, a civilian, the former governor of East Timor, Abilio Soares, was found guilty of crimes against humanity for failing to control subordinates. He was sentenced to three years in prison.

After today's verdicts, human rights experts said that the prosecutors had failed to bring effective cases. They said that important evidence gathered by Indonesia's own Commission of Inquiry on human rights violations in East Timor, and the United Nations International Commission of Inquiry, was ignored. Several witnesses from East Timor refused to appear before the court because the Indonesian government would not guarantee their security, they said.