Acting swiftly with new congressional authority, the Bush administration said yesterday that it has restored military ties with Indonesia, formally ending the last of the restrictions imposed after violence in East Timor in 1999.

The Bush administration has taken a number of steps this year to reward Indonesia, the world's most populous Muslim nation, for its cooperation in the battle against Islamic extremists. The United States resumed military training in February and sales of "nonlethal" equipment in May. President Bush also issued a statement with Indonesian President Susilo Bambang Yudhoyono in May that "normal military relations would be in the interest of both countries."

But lawmakers and congressional aides said yesterday they were surprised the State Department eliminated the remaining restrictions barely a week after Congress approved an appropriations bill that gave Secretary of State Condoleezza Rice the authority to waive them. One Senate staff member said lawmakers had anticipated a six-to-nine-month deliberative process, during which the administration would use the possibility of a waiver as leverage to extract concessions from Indonesia.

The State Department cited the "national security interests" of the United States as the reason for waiver, noting that Indonesia plays a strategic role in Southeast Asia and is a "voice of moderation in the Islamic world."

"This is an abuse of discretion and an affront to the Congress," said Sen. Patrick J. Leahy (D-Vt.), the author of legislation tying military aid to human rights conditions. "To waive on national security grounds a law that seeks justice for crimes against humanity -- without even obtaining the Indonesian government's assurance that it will address these concerns -- makes a mockery of the process and sends a terrible message. The Indonesians will see it as a clean bill of health."

The restrictions, which affect foreign military financing and sales of lethal items, are largely symbolic; Indonesia currently receives $1 million in military financing for its navy and appears to have no plans to obtain lethal items. State Department officials stressed that the decision does not trigger new assistance and the quality and quantity of any sales will be guided by Indonesia's willingness to address rights concerns.

Human rights experts and congressional aides said the Indian Ocean tsunami, which devastated Indonesia's Aceh region, had helped lessen objections to restoring military ties. Other factors included the government's peace pact with Aceh rebels, counterterrorism cooperation and the fact that the FBI has received renewed cooperation in investigating an ambush in Timika, in Papua, where two Americans were killed.