N Navin Kumar, the accused, allegedly sexually abused the girl, a std-8th student, said inspector Y Narsimha Reddy.
The girl informed her parents last evening. The parents and local residents went to the school and some of them allegedly roughed up the principal, police said.
Police today registered a case against the principal under relevant sections of IPC and Protection of Children From Sexual Offences Act.
Police didn't confirm if the principal had been detained or arrested.