Battles broke out as armed paramilitary police moved towards a mosque, whose leaders have been accused of links to Somalia's Islamist Shebab, insurgents who massacred 67 in Nairobi's Westgate shopping mall last month.
Angry protesters took to the streets after unknown gunmen assassinated a popular Muslim preacher and his three companions in a drive-by shooting late yesterday, a killing that mirrored the murder of another extremist cleric last year that provoked days of deadly riots.
A Salvation Army church was torched, but firemen brought the blaze under control.
Mombasa is Kenya's main port and a major tourist hub, popular with visitors coming to enjoy the white sand beaches on the Indian Ocean coastline.
Riots, which began after midday Muslim prayers, had largely calmed by late afternoon with Kenya's national crisis centre reporting only "sporadic violence" and stone-throwing youths.
The crisis centre said three people died of stab wounds, while the Red Cross said another hit by gunfire died in hospital. Seven others were wounded.