Police said they raided the Masjid Musa mosque acting on intelligence that a meeting to recruit militants was going on.
A reporter at the scene saw police shoot and kill one person as they tried to disperse a growing crowd screaming "Allahu Akbar" or "God is Great" outside the mosque, which has been the recent site of violent confrontations between young Muslims and police.
Police later occupied the mosque and its precincts, Kitur said.
"We have arrested dozens of youths who attacked our officers while on duty at the mosque and they are under interrogation," he said. "We have recovered a rifle that was robbed from one of our officers in the exercise. The officers were on a mission to remove radical paraphernalia from the mosque when they faced resistance."
Henry Ondieki, the Mombasa chief of criminal investigations, said police forcibly entered the mosque after getting intelligence that a meeting to recruit militants was underway. "This was not a normal day of prayers," he said. "Their intention was clear: they were planning to recruit and attack innocent Kenyan civilians.