A group of youths with machetes and knives killed three people on Kenya's coast after police raided two mosques that officials said were used to recruit Islamist militants, police said on Tuesday.

At least two of the three were Christian.

About 10 youths chanting "Allahu Akbar", or "God is greatest", killed a shopkeeper who tried to close his store in case of a riot, police had said late on Monday. The man's brother said he was Christian. On Tuesday, police said two more people had been killed, at least one of them Christian.

Police had raided two Mombasa mosques on Monday, seizing weapons and literature, which officials said was evidence of militant activity. They shot one man dead, who they said was trying to attack them, and arrested 251 other people.

Kenya has been trying to break up the militant networks that it blames for a series of attacks on its coast and the port city of Mombasa, saying many of the recruits have been inspired by al Qaeda-linked Somali Islamist group, al Shabaab.

Mombasa county police commander Robert Kitur said the youths had killed the two other men when they attacked people on public transport. Two more people were wounded, he said.

"We have launched an operation which is still ongoing, and so far we have arrested 16 suspects," he said, referring to detentions related to violence after the raid.

The detainees were expected to be charged on Tuesday, he said.

Civil rights groups say police have been targeting Muslims unfairly, deepening distrust in a community which already accuses the government in mainly Christian Kenya of sidelining them.

Police raids in the past on other mosques, which officials suspect of being used as recruitment centres, have sparked violent protests.