Citing doctors, police said repeated sexual assaults were carried out on the boy and he might have been killed to hush up the matter.
They also detained five teachers for interrogation over the murder.
The deceased was identified as Abir Hossain, 11, a Class-II student of Nurani Hafizia Madrasa and Orphanage, and son of Ali Hossain of Kotchandpur upazila in Jhenaidah district.
On information, police recovered Abir's body from a mango orchard in the morning and sent it to a local hospital for autopsy, said officer-in-charge of Alamdaga Police Station Asaduzzmana Munshi.
Madrasa Principal Mufti Abu Hanif said the boy had been missing since Tuesday's Maghrib prayers.
At a press briefing in the afternoon, Superintendent of Police of the district Mahbubur Rahman claimed that the madrasa boy had repeatedly been molested which was evident in the postmortem report. “He might have been killed to hush up the matter.”
He also said they detained five teachers of the madrasa for interrogation over the matter and their fingerprints were sent to Dhaka for DNA test.
Police and locals said Nurani Hafizia Madrasa and Orphanage was established a few years back it has not a total of 71 students.
Muhtamim Mufti Abu Hanif said Abir’s mother Kamela Khatun enrolled him in the madrasa one year back. He went missing on Tuesday.
Residential Medical Officer at Sadar Hospital Dr Shamim Hosssai said they found signs of sexual torture on the victim’s body.
Meanwhile, a special team of Rapid Action Battalion (Rab) along with two dog squads rushed in from Dhaka and launched a manhunt for the severed head.
However, they could not find it till the evening.