The incident occurred on Friday at Budakhunta UGME School in Oupada block in Odisha's Balasore district.
The inquiry by district education officer revealed that the headmaster had been to a training programme in another place on that day and had allegedly telephoned a teacher of the school that Vajpayee has passed away.
He had also asked his junior teachers to conduct condolence meeting in the honour of the former prime minister and the school was closed for a day, the official said.
The erring headmaster has apologised for the blunder.