The United States has begun to restore security relations with deeply troubled Indonesia, the world's most populous Muslim nation and one that sits alongside the vital shipping lanes through the South China Sea in Southeast Asia.

The State Department announced two weeks ago that a ban on defense exports to Indonesia had been lifted. That was the third step taken over the past year, a ban on non-lethal military exports having been lifted in May and the resumption of military education having been decided in February.

Adm. William J. Fallon, commanding officer of the Pacific Command at its headquarters in Camp H.M. Smith, said in an interview that he was pleased with the decision, because "it's in our best interests."

The admiral, who had been quietly lobbying the State and Defense departments and Congress to adopt a new policy, said his staff and the U.S. Embassy in Jakarta were drawing up lists of "exactly what to do with this opportunity."

Fallon said he didn't want to get out ahead of the process, which will require agreement with Indonesian leaders, but suggested that enhanced maritime security would be a priority. On a mundane level would come spare parts for U.S. equipment that Indonesia had acquired but which sorely needs repair.

The State Department announcement said the new policy was intended, among other things, to "support U.S. and Indonesian security objectives, including counter-terrorism, maritime security and disaster relief."

The United States, under pressure from human rights activists and Congress, cut security relations with Indonesia in the 1990s to protest Indonesian army abuses during East Timor's struggle for independence. The army had also been accused of abuses against separatists in Aceh at the western end of the archipelago of 6000 inhabited islands.

"The U.S. remains committed to pressing for accountability for past human rights abuses," the State Department said, "and U.S. assistance will continue to be guided by Indonesia's progress on democratic reform."

Fallon said several times that his command was "sensitive" to those violations of human rights.

Many U.S. officers have been eager to resume a program called International Military Education and Training, as it was perhaps the most effective way to influence Indonesian officers on the missions and behavior of the armed forces in a democratic nation.

Indonesia's president, Susilo Bambang Yudhoyono, may be a case in point. He is a retired army general who attended two U.S. military schools and once trained with the 82nd Airborne Division. He is regarded as a reformer who has sought to get Indonesia's armed forces out of politics.

Indonesia's troubles are many — terrorism led by Jemaah Islamiya, or JI; piracy in nearby waters; the devastation caused by the tsunami last December; and threats to public health from avian flu and AIDS.

When Indonesian police raided a JI hideout in early November and killed a leader named Azahari bin Husin, they found the terrorists planning to attack Americans, Australians, and other Westerners in Jakarta.

"Specifically," the State Department said in a travel warning, "they discovered 35 bombs prepared and ready to use."

The JI, which is allied with the al-Qaida terrorists led by Osama bin Laden, is believed to have set off bombs in Bali in 2002, in a Jakarta hotel in 2003, near the Australian Embassy in Jakarta in 2004, and three simultaneous explosions on Bali on Oct. 1 this year.

The terrorists seek to establish a united Islamic state that would comprise Indonesia, Singapore, Muslims in southern Thailand, Malaysia, Brunei and Muslims in the southern Philippines.

Such a state could seek a chokehold on the South China Sea's shipping lanes through which pass more ships each year than those transiting the Suez and Panama canals combined.

A more immediate threat arises from pirates. The International Maritime Bureau, with headquarters in Malaysia, reported that Indonesia was the site of 61 episodes of piracy in the first three-quarters of 2005, which was the highest in the world.

In 1994, Indonesia experienced only 12 instances of piracy but six years later, in 2000, that had risen to 90 cases. The incidents declined this year, the maritime bureau said, because there were no reported incidents for two months after the tsunami.

Those incidents were also down, the bureau said, "due to the Indonesian authorities launching a full-scale maritime operation code named 'Gurita 2005,' which commenced in July." Even so, 50 Indonesia sailors have been taken hostage, the bureau said, and pirates were attacking vessels farther out to sea and closer to Malaysian waters.

Honolulu-based Richard Halloran is a former New York Times correspondent in Asia.