According to the police, the incident occurred on August 16 when Irfan Ali (36), hailing from Bihar, had allegedly crumbled the small flag in an attempt to wipe his face.
A case was registered against him under section 2 of the Prevention of Insult to National Honour Act after a student brought the matter to the notice of the school administration which, in turn, informed the police.
The accused has been lodged in prison for the non-bailable offence, police said.