U.S. Assistant Secretary of State James Kelly is in Indonesia, for talks on security measures and anti-terrorism efforts. But the visit comes amid a new controversy over the U.S.-led war on terror.

The American envoy arrived in Jakarta Friday amid a flap over a U.S. Justice Department decision to add Indonesia to a list of countries whose male citizens must register and be fingerprinted when visiting the United States. The new immigration policy is aimed at tracking potential terrorists.

Indonesia, the world's most populous Muslim nation, says this U.S. measure is unfairly directed at Islamic countries.

Indonesian Foreign Minister Hassan Wirajuda told reporters Friday his ministry has issued a travel advisory, warning Indonesians to postpone visits to the United States.

Indonesian officials say President Megawati Sukarnoputri raised her concerns with Assistant Secretary of State James Kelly at their meeting Friday. They say the policy is highly discriminatory and sends the wrong message about Jakarta's commitment to fighting terrorism.

But Indonesia has been the focus of concern as the Asian country most vulnerable to penetration by al-Qaida terrorists fleeing U.S. troops in Afghanistan.

The United States and many Southeast Asian countries had been critical of Jakarta for more than a year for not doing enough to investigate and detain members of Jemaah Islamiyah, a regional terrorist group with alleged links to al-Qaida.

That started to change when Jemaah Islamiyah was suspected of carrying out October's deadly bombing on the resort island of Bali. U.S. law enforcement officials are now working with a multi-national team in Indonesia on the bombing investigation and a number of key suspects have been arrested.