Indonesian security forces have used tear gas and clubs to break up a large demonstration near the Defence Ministry in the capital, Jakarta.
Violence also broke out in the east of the country where more than 1,500 people went on the rampage, shouting "Burn Chinese shops!"
At least three students were injured and dozens were arrested in the clashes in Jakarta. The demonstrators were demanding an end to the military's role in domestic politics and for disgraced former President Suharto to stand trial on graft charges. One group of about 200 protesters managed to get into the presidential office compound in central Jakarta.
Elsewhere in the capital, hundreds of students brought rush-hour traffic to a standstill as they demonstrated on the main city road and about 1,500 more protested outside the attorney-general's office to demand Mr Suharto stand trial.
Meanwhile, in Samarinda, an oil town in the Indonesian part of Borneo island, more than 1,500 people attacked shops owned by ethnic Chinese. The rioting erupted after a strike by about 500 transport workers demanding cheaper spare parts. Ethnic Chinese, the country's most economically successful minority group, have been repeated targets of attacks.
Education Minister Juwono Sudarsono blamed the repeated rioting across Indonesia on new political freedoms. He said he had asked the government to ban street rallies during next June's general election and restrict campaigning to indoors to reduce bloodshed.
Many Indonesians hope the election, to be followed by a presidential election, will usher in a new era of democracy after 32-years of autocratic, army-backed rule under Mr Suharto.
Mr Suharto's reign ended in humiliation and chaos in May amid bloody rioting, political turmoil and economic crisis. More than 100 new opposition parties have sprung up in the post-Suharto era.
But Mr Juwono, once considered a moderate, said the recent unrest showed Indonesia lacked the social and economic foundations for political freedom. "The pendulum has swung too much in favour of political openness," he added.
"This desire for political democracy and openness, juxtaposed with a period of endemic economic deprivation... this combination is about the most dangerous possible for political stability."