The accused identified as Murugan, headmaster of a Panchayat Union Elementary School at Periyanarikottai near here, was arrested following complaints from parents and locals.
There were only two teachers in the school, including the headmaster, where 16 children were studying, police said.
On a complaint from one of the parents yesterday, Assistant Education Officer Poosaidurai and Additional Superintendent of Police Vandita Pande conducted inquiries.
Poosaidurai said the children would continue to receive education in the school as steps were taken to appoint another teacher in the institution.