Accused Panchu Sahu worked at Surat and had come home at Bhetani village in Aska area for his daughter's wedding when he committed the offence on Sunday, they said.
The accused, who raped the 12-year-old girl when she was alone at home, was arrested yesterday.
Sahu and the victim were sent to MKCG Medial college and Hospital at Berhampur for examination, police said.