Radheshyam Netam, principal at a higher secondary school in Ghanora village, around 250 kms away from here, was apprehended on a complaint by the 16-year-old victim, Kondagaon SP D Shravan told PTI over phone.
Police said the incident took place in April in the premises of the school.
"The accused Netam had threatened the Class X student not to disclose the incident," the SP said.
However, she narrated her ordeal to her parents few days after the rape following which her parents approached a local panchayat seeking suitable action.
The SP said the district administration came to know about the incident recently and the investigations started leading to Netam's arrest.
A case has been registered against Netam, he said.