Modhiar Siddique Ali of the Natham mosque, arrested on a complaint from the father of the victim, had also video-graphed his act using mobile phone and blackmailed the boy, they said.
During the investigation police found that Ali had sexually harassed the boy for more than one year.
Though the boy's mother had complained to the local Jamath, no action was initiated against Ali.
Besides booking Ali, police have registered a case against Jamath president Abdul Ajeez and correspondent Jahangir and member Sirajuddin for allegedly covering up the crime.