Anne Gearan, Jakarta – Secretary of State Condoleezza Rice said Indonesia has earned the restoration of close military ties with the United States, despite complaints from human rights groups that the move betrayed victims of military brutality.

The United States lifted a six-year arms embargo last fall and re-established other military ties with the world's most populous Muslim nation, which the Bush administration views as a key ally against terrorism. The ban was imposed in 1999 after Indonesian government troops ravaged East Timor during the territory's break from Jakarta.

En route to Indonesia, where she arrived Monday, Rice cited Indonesia's cooperation in anti-terror investigations as well as democratic progress.

"The military is an important institution in Indonesia," Rice told reporters on her plane. "It's by no means completely made its reform, but we believe those reforms are underway and that we can have a more positive effect on the reforms by being part of it."

Rice's first visit here as secretary of state will include a speech on democracy in the Muslim world and the similarities between two trade-oriented multiethnic democracies. She is visiting an Islamic school and meeting with Indonesian President Susilo Bambang Yudhoyono, a US-educated former general.

"You want to be careful not to cut off contacts with the very people who are going to be important for the restoration of democracy," Rice said.

Al-Qaida-linked militants have launched a series of deadly bombings on Western targets in Indonesia since 2002, including suicide attacks last year on three crowded restaurants on Bali island that killed 20 people.

The Bush administration had long wanted to lift the arms embargo, but it was stymied by US lawmakers demanding the military undertake meaningful reform.

Citing national security concerns, the State Department used recently granted powers to waive the restrictions in November. But that action has prompted complaints from human rights groups.

"This is a profoundly disappointing and sad day for human rights protections everywhere," John Miller from the East Timor and Indonesia Action Network said then. "With the stroke of a pen... President Bush betrayed the untold tens of thousands of victims of the Indonesian military's brutality." In a letter to Rice last week, the New York-based Human Rights First asked her to link US military aid to real progress in reform.

Yudhoyono, elected in 2004 in the country's first-ever direct elections for head of state, visited Washington twice to lobby for lifting the ban.

Defense Secretary Donald H. Rumsfeld said last week the United States "lost a generation of relationships" with the Indonesian and Pakistani militaries because of sanctions. Most military ties with Pakistan were severed during the 1980s because of its nuclear weapons program.

Rumsfeld said it's important that the United States "not complicate efforts to build useful relationships with nations that can aid in our defense." He said the US military had to renew the ties with these large predominantly Muslim countries "almost from scratch" following the terrorist attacks of Sept. 11, 2001.

Rumsfeld said he understands the reason why the sanctions were imposed. But, he added, "I think it's something that we need to think very carefully because as a result of some of those actions the United States is looked at as a less than perfectly reliable friend and ally."

The Indonesian military has long been accused of human rights violations as it put down separatist insurgencies in far-flung regions of the sprawling archipelago. While Jakarta did hold trials for some of those accused in the East Timor violence, 16 of the 18 government and military officials involved were acquitted. That sparked outrage among Western governments and rights groups who labeled the rights court a failure.

The US and Indonesian militaries had close ties during the three-decade rule of the dictator Suharto, whose regime collapsed in 1998 amid riots and an economic meltdown, ushering in democracy.

Indonesia's invasion of East Timor in 1975 and the subsequent 24-year occupation is blamed for the deaths of 200,000 people – a third of the population. Anti-insurgent activities in the eastern province of Papua since 1969 are believed to have caused the deaths of more than 100,000 people.