Rioters protesting at the killing of a prominent Muslim cleric torched a Christian church and clashed with police in Kenya's Port town of Mombasa.

A group of young Muslim protesters took to the streets after Friday prayers, burning tires and blocking the main road into the city, Reuters reported.

"They have burnt the Salvation Army church and we are now trying to repulse them with tear gas," a senior police officer told AFP.

The Red Cross said four people were killed and seven wounded during the disturbances.

Hundreds of riot police officers were deployed in the Muslim neighbourhoods of Marengo and Kisauni, after the assassination of Sheikh Ibrahim Ismael, also known as Ibrahim 'Rogo' Amar, whose death was blamed on police.

"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."

Ismael was gunned down in a hail of bullets with three other people on Thursday night as they were driving home after preaching at the Masjid Musa mosque.

Ismael was said to have links with al-Shabaab, the terrorist group that laid siege to the Westgate mall in the capital Nairobi, killing more than 60 people in September.

The assassination happened just a few hundred metres from where Ismael's predecessor, Aboud Rogo Mohammed, was shot dead last year.

Rogo was accused by the Kenyan government and the US of using his preaching at Masjid Musa to recruit young jihadists for the Somali-based al-Shabaab.

His assassination sparked three days of violence, as Muslims pointed the finger at police and foreign secret services.

Muslim leaders have accused Kenyan anti-terror police of launching a campaign of assassinations against terror suspects, of which Ismail was the last victim.

Police have denied the allegations.

Mombasa Violence
A police officer outside the Masjid Mussa mosque during an operation to to suppress demonstrators reacting to the killing of an Islamic cleric (Reuters)