The three were arrested after a detailed questioning, police said.
34-year old Mohammed Riyas Maulavi, a Muezzin (the official who proclaims the call to prayer) and Madrassa teacher from nearby Choori had been murdered on Monday by a gang of persons who entered the compound of Muhayuddin Juma masjid of Choori and allegedly slit his throat in his room.
Special squad led by Kannur Crime branch Superintendent of Police A Sreenivas, investigated the case.
The accused were produced before local court and remanded to judicial custody.