Hardliners in Indonesia have threatened violence
At least four people were injured, including a policeman who was taken to hospital in an ambulance.
It was the second day of protests by groups of radical Muslims opposed to the US-led military action in Afghanistan.
And about 5,000 Filipino Muslims have staged their biggest anti-American protest so far on the island of Mindanao in the southern Philippines.
The peaceful protest included religious leaders, students and local politicians. They burned American flags and called for a holy war in support of Osama Bin Laden and the Taleban.
They also distributed leaflets urging President Gloria Arroyo to withdraw an offer to the Americans to let them again use former military bases in the Philippines.
The US State Department has cautioned Americans against travelling to Mindanao, where Muslim insurgents have long been battling for an Islamic state.
Muslims make up about 5% of the Philippines' 76-million population but they are largely concentrated in the south of the country.
Violence
Security in the Indonesian capital remained tight on Tuesday, with US and British residents warned to keep a low profile. The British Embassy has reopened, but the US embassy and surrounding road remains sealed off by huge barbed wire barricades.
Some protesters have been camped outside the US embassy since Monday.
One extremist group, the Islamic Defenders Front, is calling for a jihad (holy war) against the United States and has vowed to continue its demonstration until all Americans have been expelled from Indonesia.
It has called on the government to cut diplomatic ties with Washington by Wednesday or it threatens to attack American interests and civilians in the country.
"We will call on Muslims to conduct sweepings against foreigners," the group's leader, Habib Muhammad Riziq Shihab, told AFP.
President Megawati Sukarnoputri was the first Muslim leader to visit Washington in the aftermath of the 11 September attacks, when she gave her support to President Bush's war on terrorism.
But she has to be mindful of the strength of anti-US feeling in Indonesia, which is the world's largest Muslim nation.
Growing unrest
Our correspondent in Jakarta says the protests are getting bigger, after a peaceful day of protests on Monday.
Earlier, about 200 members of the Indonesian Muslim Student Action Unity held a rally outside the United Nations building in Jakarta, broadcasting anti-US speeches from the back of a truck.
"America the real terrorist," said one poster.
There were small anti-US protests across Indonesia.
In the city of Makassar on Sulawasi Island, 1,400km (870 miles) northeast of Jakarta, dozens of demonstrators burned a US flag and threatened to round up and expel US citizens.
And in the Javanese city of Bandung at least 2,000 people held a protest march, said police.