The cleric returned to the village yesterday, police said, adding that he was allegedly abducted and tortured.
Ali told the police that he was taken to an unknown place by his abductors and later dropped off at Kota railway station.
A STF team led by Deputy Superintendent of Police Amit Kumar had arrived in Meerut two days back to search for the missing cleric.
Ali, who preaches at a madrasa in Rajasthan, went missing when he had gone to Muzaffarnagar railway station to book a ticket last week.