Four people were killed when supporters of a slain radical Muslim cleric clashed with riot police after setting fire to a church and burning tires in Kenya's main port city of Mombasa, the Kenya Red Cross said. 

Sheikh Ibrahim Omar was shot dead Thursday night, igniting religious tensions in the commercial and tourism hub in east Africa's largest economy, two weeks after Islamist militants killed at least 67 people in a raid on Nairobi's Westgate shopping mall. Omar's followers blame security forces for his death.

Kenya riot police

A Kenyan policeman removes a rug which was set on fire by youths protesting the killing of an Islamic cleric in the coastal Port town of Mombasa. (Joseph Okanga/Reuters)

He preached at a mosque that has in the past been linked to the Somali al-Shabaab Islamists who claimed responsibility for the shopping centre attack.

Omar was found dead in a car hit by more than a dozen bullets, television images showed.

Youths torched a Salvation Army church and temporarily blocked the main road into the city, a witness told the Reuters news agency.

Kenyan police in riot gear fired gunshots and teargas to break up the crowd.

The worst of the running battles with police took place in Mombasa's downtrodden Saba Saba neighbourhood, where traders shuttered their shops and residents fled for safety.

"We are trying to deal with some youths who have started bringing trouble within town," Robert Kitur, Mombasa county police chief, told Reuters. "They are few. We will contain them."

Strikingly similar attack

The imam was shot in Mombasa's outskirts on the main road to the resort town of Malindi, a few hundred metres from where another firebrand cleric, Aboud Rogo, was shot dead in his vehicle in August 2012 in a strikingly similar attack.

Both Kenya and the United States had accused Rogo of recruiting and fundraising for Somalia's al-Shabaab militants.

Rogo's death last year unleashed deadly riots in Mombasa's rundown neighbourhoods where he commanded a loyal support base.

Both imams were popular among youths in Mombasa and along Kenya's Indian Ocean coastline where many Muslims feel marginalized by the predominantly Christian government.

"This is no doubt a police execution given what has happened in Nairobi," said Abdul Hassan Omar, 37, in Mombasa's rundown Majengo district, where Omar and Rogo both preached.

Kitur dismissed the accusation and said officers would stop any protests after Friday prayers getting out of control. "The police have nothing to do with the shooting. That's not how we operate," he told reporters.

The Sept. 21 assault on the Westgate mall was the worst militant strike on Kenyan soil since al-Qaeda bombed the U.S. Embassy in Nairobi in 1998. The raid shocked Kenyans and the world and has raised questions over intelligence failures.

"They [authorities] have panicked because of their own laxity which killed Kenyans at Westgate. Now they are trying to save face by sacrificing innocent Muslims," said Hatib Suleiman, 21, who prays at Omar's Masjid Mussa mosque.

"We are not going to take this lightly."

Al-Amin Kimathi, chairman of the Muslim Human Rights Forum, said Omar had been a student of Rogo and had publicly espoused the rigid ideological beliefs of his former mentor.