The incident created tension in the village on Sunday as the boy's family alleged that the man, identified as Bhikan Pinjari, had sodomised the minor, a son of his neighbour in Islampura locality.
However, police didn't confirm this allegation, saying the matter is under investigation.
According to police, the boy went missing from the locality on Saturday morning, following which his parents lodged a missing person complaint with Pimpalgaon police.
His body was found last night in the vicinity of Islampura.
After the boy's body was found, his parents and other neighbours caught hold of Pinjari and thrashed him. He was admitted in Nashik civil hospital yesterday after police intervened into the matter.
Desale said the police are also investigating an allegation by some villagers that Pinjari's mother practices 'witchcraft' and have also detained her.
So far, police have registered a case under section 302 (punishment for murder) of the IPC and not added the section of unnatural offences as the investigation is on, the officer said.
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