Tension remains high in Kenya's port city of Mombasa after riots in protest at the murder of a prominent Muslim cleric on Thursday left four dead, about eight injured and the Majengo Salvation Army Church razed on Friday.

It is just over a year since the church suffered a similar attack after the murder of another prominent cleric under similar circumstances.

Unknown gunmen sprayed bullets at the vehicle in which Ibrahim "Rogo" Omar and four others drove home after evening prayers at Musa mosque on Thursday.

The cleric and three of his passengers died. The motive for the murder is unknown. However, it appears Omar had links with Al-Shabaab, the group responsible for the four-day siege on the Westgate Mall in Nairobi that left close to 70 people dead and nearly 200 injured in September.

Omar was widely believed to have taken over from controversial cleric Aboud Rogo whose death under similar circumstances in August last year led to several days of violence in Mombasa. The Salvation Army church along with four other churches suffered extensive damage then too.

"When they burnt the church building last year, we incurred damages of over 1.5 Million Kenya Shillings (approximately $17,500). This time the damage is worse," said Major Emmanuel Mutepe, Head of Majengo Salvation Army Church.

The events in Mombasa came in the midst of religious tension in the East African nation following the siege in Nairobi.

Abubakar Shariff Ahmed, a Muslim cleric, told AFP he blamed police for the shooting of Ibrahim Omar and said it is a "war against Islam".

Some victims of Friday's Mombasa riots told local media from their hospital beds that they were singled out on religious grounds. One victim receiving treatment for three stab wounds in the local hospital told local media, "I was running away from the chaos when I met a group of the rioters. They demanded to know if I was Muslim or a Christian but stabbed me as I tried to defend myself."

Rev Lawrence Dena, in reaction to the riots and the razing of the church made a statement on behalf of a joint forum of Mombasa pastors, saying, "The Church has noted with concern the continued targeting of its members and we are putting the government and Muslim leaders to task. We are asking the government and Muslim leaders to explain why Christians are being attacked as witnessed both in the Westgate and Majengo."

"We wonder what connection the [Muslim cleric's] killing has with the church or with church facilities so that every time an incident like this happens, churches are torched and vandalised," said church leaders of the Kenya National Congress of Pentecostal Churches and Ministries in a media release following the destruction of the Majengo Salvation Army Church.

Mombasa Deputy Governor, Ms Hazel Katana, criticised police for laxity in responding to threats of impending violence. "This particular church, the Majengo Salvation Army, has been attacked before and one would imagine that the police would have taken extra care and run here to guard this area," she told media.

A section of Muslims including the Supreme Council of Muslims in Kenya has spoken out strongly against the violence that has since been quelled.