Shops and restaurants in central Colombo were shuttered following the riots in two mainly Muslim coastal resorts popular with international tourists that left four people dead and Muslim homes and businesses razed.
"The protest is against the BBS and the police failure to protect our community," a Muslim shopkeeper who declined to be named told AFP.
"We are also asking the government to take action against those behind the riots."
A Sinhalese businessman said most of the shops in the normally bustling Pettah wholesale market in Colombo were closed.
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The closures came as police said a moderate monk, Watareka Vijitha, who voiced opposition to the BBS had been abducted, beaten up and dumped by the roadside outside Colombo early today.
Hospital sources said the monk was in intensive care. Residents found him stripped naked, hands tied behind his back and dumped by the roadside in Panadura, a town outside the capital, police said.
The BBS, which has denied it was behind the riots, has been accused of targeting Buddhist clergy who opposed their hardline tactics.
During a tour of riot-hit Beruwala, Rajapaksa promised an investigation into the riots and appealed to Muslims not to go ahead with a "hartal" or strike, plans for which had been circulating among Muslim communities.
The riots are the latest in a series of religious clashes to hit the island following unrest in January and last year, when Buddhist mobs attacked a mosque in Colombo.