The accused, identified as Rabindra Panda alias Rabinana (45), is absconding, the police said.
The incident took place when the girl, a class 10 student, went to the temple on Monday noon to collect 'prasad'.
The priest took her to the kitchen adjacent to the temple on the pretext of giving her prasad and allegedly raped her there. The accused also warned her against telling anyone about the act, the police said.
"After preliminary medical examination, doctors informed us that it was a case of sexual assault and accordingly a police team went to the hospital," Sudarshan Dash, inspector-in-charge (IIC) of Dharmasala police station.
A case under section 376 of IPC and 4 Protection of Children from Sexual Offenses Act 2012 has been registered against the accused.