Six people, including the opposition leader and former deputy prime minister Anwar Ibrahim, were detained under the Internal Security Act (ISA), a draconian piece of legislation thata allows suspects to be held indefinitely without trial.
About 40 others were arrested after police used tear gas and water cannon to break up a crowd of Mr Anwar's supporters who were demanding the resignation of Mahathir Mohamad, the prime minister.
Plain-clothes police kicked and beat the demonstrators who have turned out in large numbers all over Malaysia since Mr Anwar was dismissed as deputy prime minister early this month for alleged homosexuality and treason.
For several hours the state television company prevented foreign broadcasters, including the BBC, from transmitting footage of the disturbances.
Offices around the city were closed early and traffic was reduced to a crawl as main roads were sealed off by police in an attempt to prevent the demonstrators from regrouping.
At the National Stadium, hundreds of police were on duty at the official closing of the Commonwealth Games by the Queen. Lawyers and human rights organisations said it was the worst crackdown since 1988 when 106 people were arrested under the ISA and four newspapers were closed during a similar challenge to Dr Mahathir's authority.
"I feel very sad because Dr Mahathir is a great leader," said Azizah Ismail, Mr Anwar's wife, who takes over the leadership of his reform movement. "But now he has become a political desperado who is willing to suppress his own people just to keep power."Reuse content