Apparently desperate to relieve himself, Ranjan had urinated in a mug and left it near the classroom.
His father has lodged a complaint with the police against the teacher and the school administration.
The teacher has gone on leave following a public uproar over her alleged action. The school is yet to comment on the punishment, but faces a government probe.
"I have been asked to inquire into the matter and submit a report to the district education officer. I have spoken to the boy and his parents and will meet the school management soon," said mandal education officer Somi Reddy.