It is the first time since demonstrations for political change began last month that the protests have ended in violence.
Police used tear gas and water cannon after a large crowd gathered chanting for reform.
![[ image: width=150]](/olmedia/200000/images/_200633_hair_pull_150.jpg)
The protesters responded by throwing rocks and stones, and a series of clashes followed.
Police in balaclavas chased people through department stores, beating some of them.
The city's police chief said his men had seized several petrol bombs and hundreds of pamphlets calling for reform.
The BBC Kuala Lumpur correspondent says the authorities are clearly determined to clamp down on any form of dissent, with an Asia-Pacific summit due to be held in the Malaysian capital in three weeks.
Chemical irritant
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The worst trouble began after evening prayers in the Kampong Bahru district of the city.
Pro-reform demonstrators threw stones and rocks at the police, who responded by firing tear gas and water cannon containing a powerful chemical irritant to break up the demonstration.
Protestors later regrouped in another location and again water cannon was used to disperse them.
Some of the demonstrators regrouped, and there were violent scenes as police - some plain clothed, others in balaclavas - arrested people in the crowd, including several women.
Demonstrations in support of Mr Anwar have been declared illegal and several people were arrested in a series of anti-government rallies that followed Mr Anwar's detention.
Most were since released on bail, but police are now warning those who join the protests that they could face arrest under the Internal Security Act, which allows for indefinite detainment without trial.
![[ image: width=150]](/olmedia/200000/images/_200568_mal150.jpg)
Mr Anwar was sacked by the Prime Minister, Dr Mahathir Mohamad, last month. He was later arrested, after which, he says, he was beaten by police.
He faces trial next month on four out of 10 counts of corruption and sodomy - charges he says are part of a high-level political vendetta.
One of the two main witnesses against him now says he was stripped, humiliated and brainwashed in custody before telling police he had committed sodomy with Mr Anwar.
Mr Anwar's wife has called for foreign observers to be allowed to attend the trial after the prime minister reportedly said that they would not be permitted in court because it would put pressure on the judges.
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