Police were forced to fire in the air and lob teargas to eject the group of youths who forced their way into Masjid Swafaa mosque in Kisauni for prayers.
The mosque is among four closed in the past week following police raids that netted over 200 suspects and believed to be linked to radicalisation.
Others closed are Masjid Shuhadaa, Sakina and Minah mosques where firearms and explosive materials were seized.
More police officers have been deployed to patrol Mombasa streets following reports of a planned demonstration later on Friday over the mosque raids.