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 shop-keeper 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.
The violence on Sunday and Monday nights was blamed on the hardline Buddhist Force (BBS) in the southern towns of Alutgama and Beruwala, about 60 kilometres south of Colombo.
The closures came as police said a moderate monk who voiced opposition to the BBS had been abducted, beaten up and dumped by the road side outside Colombo early Thursday.
The monk's condition was not immediately known. He was found by residents with his hands and legs tied in the town of Panadura, a police spokesman said.
The BBS, which has denied it was behind the riots, has been accused of targeting Buddhist clergy who opposed their hardline tactics.
President Rajapakse on Wednesday urged majority Buddhists and minority Muslims to ease tensions and take steps towards peace.
During a tour of riot-hit Beruwala, Rajapakse promised an investigation into the riots and appealed to Muslims not to go ahead with a 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.
Muslims make up about 10 percent of the 20 million population, but are accused by Buddhist nationalists of having undue influence in the Buddhist-majority country.
The main Muslim party in Rajapakse's ruling coalition, the Sri Lanka Muslim Congress (SLMC), boycotted parliament on Wednesday, accusing authorities of failing to control the BBS.
Police said the situation was returning to normal in the troubled resort areas on Thursday, but troops and police were patrolling the streets to deter further violence.
The United States has led international condemnation of the violence, while Western embassies in Colombo have advised nationals holidaying in the area to stay indoors.
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@baby doll main sone di: After LTTE, you guys started using BBS. Well, that's what your definition of peace with neighbors.
Muslims are safer in Syria, Iraq, Pakistan and Afghanistan not in Sri Lanka?
@ps: Why Muslim have problem in every non Muslim country? " what will happen if Muslim businessmen leave permanently?" I say why they are not leaving? Do it at earliest to teach lesson to all non Muslim. There is no other way to teach non Muslim a lesson. I am dreaming all Non Muslim country (USA/Canada/West/India/Burma etc) collapsing because all Muslim left those country & migrate to Nissan e Ummah Pakistan.
Muslims may make up only 10% of the population but they enjoy 20% of the national income. They are an entrepreneurial lot. The BBS consists of jealous people. They admit it themselves when they say they want to curtail Muslims power over the economy and government.
Sri Lanka will suffer heavily if this goes on. A single day of protest is enough to shut down the largest market in the island. Imagine what will happen if Muslim businessmen leave permanently? Worse still would be another ethnic war. 30 years of fighting the LTTE doesn't seem to have taught these sinhalese extremists anything.
good this is the only way muslims will lwarn to behave