"We conducted a security operation in the mosque, we will give details later," said Richard Ngatia, the senior officer in the district of Kisauni where the raid took place.
It came just two days after police raided mosques in the same city searching for weapons and radical supporters of Somalia's al Qaeda affiliated Shebab militants.
According to another police source, who wished to remain anonymous, grenades, bombs, oil and ammunition were discovered in the latest raid.
On Monday, security forces targeted the Masjid Musa and Sakina mosques in Mombasa.
These raids resulted in the death of a 20-year-old, who police said had tried to throw a grenade at security forces and the arrest of more than 200 people.
Thirteen of those arrested have been charged with possession of explosive materials and pleaded not guilty.
The two mosques have been closed since Monday's security operation.
Following the raid, four people were stabbed to death in apparent revenge attacks.
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