The incident occurred on Thursday but the student, Dipankar Das (15), never returned home and his body was found floating in the Churni river this morning.
A student of Anil Smriti High School at Krishnaganj, Dipankar was caught copying red handed in the examination hall and his answer script had been taken away.
The school headmaster Samir Kumar Dawn said he contacted Dipankar's father Nikhil Das and asked him to meet him at that time.
"The guardian informed me he would meet me on Monday and requested to leave his son. So we left him," Dawn said.
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But Dipankar did not go back home. On returning home late in the evening, Das went out in search of his son but could not find him.
He and some other guardians met the headmaster yesterday and demonstrated. A missing diary was also lodged with Krishnaganj police.
Dipankar's cycle and school bag were spotted at the bank of Churni river near a burning ghat at Krishnaganj on yesterday afternoon. His body was found floating near the burning ghat this morning.
Das blamed the school authorities for the death of his son.