The protests brought business in the busy tourism resort city of Mombasa to a standstill as many businesses were hurriedly closed due to the chaos, Xinhua reported.
Sheikh Rogo, an ally of slain controversial cleric Aboud Rogo, and three others were killed by unknown gunmen Thursday night when their vehicle was sprayed with bullets.
Tension has been building up since early Friday amid heavy police presence around the Musa mosque where the slain preacher delivered controversial sermons.
One protester was shot and a Salvation Army church was torched as Muslim youths engaged the police in running battles.
Last year's killing of controversial cleric Aboud Rogo Mohammed sparked days of rioting.
The latest protests came two weeks after the Sep 21 attack on an upscale Kenyan shopping mall in Nairobi which killed at least 67 people.
The siege of the Westgate shopping mall in Nairobi is over but forensic operations at the site are still going on and armed security personnel remain on the scene.
The Kenyan police have vowed to step up surveillance across the country following intelligence reports that Somali militants who claimed responsibility for the recent mall attack were planning to carry out further attacks in the East African nation.
Police Inspector General David Kimaiyo said security forces have increased surveillance at key installations, private and public places and urged the public to exercise caution while dealing with people with suspect motives.
Tension remains high in Mombasa with fears of retaliation from suspected Al Shabaab sympathisers.
The killing of Aboud Rogo Aug 27, 2012, sparked similar riots in the coastal city leading to the death of at least five people, among them four Kenyan police officers, and massive destruction of properties and churches.
At least eight churches were burned during violent demonstrations.
Aboud Rogo was accused by the US and the UN of supporting Al Qaida-linked militants in Somalia, forcing the UN Security Council to impose a travel ban and asset freeze on him.
Mombasa, the country's second largest city and a major tourist spot, is one of many cities targeted by a series of grenade attacks and abduction of foreigners in recent months.
The East African nation's coastal towns are the backbone of the country's thriving tourism industry. They have been hit by the fear of terror attacks and the kidnapping of foreigners by Somali pirates from resorts near the border with Somalia.
The heightened security follows a major terrorism alert that was issued by the police last month after intelligence reports indicated that Al Shabaab may be planning an attack.
--IANS (Posted on 04-10-2013)