Police arrested several youth at the Masjid Musa Mosque, where they were receiving radical Muslim teachings, the Kenya Broadcasting Corp. reported.
One suspect confessed that there were 18 guns in the mosque.
Riots and conflicts ensued in the city, and scores of youth were injured, while others were arrested.
The incident occurred a day after Principal Secretary Mutea Iringo met with police to discuss the rampant radicalization of Muslim youths in the country.
Iringo said the teachings are not based on the Koran, and said the government will deal with all those who are found spreading extremist teachings.