The accused has three children and the victim, a class V student, is the eldest child, police said, adding that the children's mother had died in a road accident two years ago.
The girl first informed about the crime to her aunt living in the neighbourhood on Friday night when the accused again tried to assault her, they said.
Her aunt then took the girl to the police station and lodged a written complaint against her father, they said.
Medical examination of the girl confirmed sexual assault, police said.
The victim also mentioned that her father had threatened to kill her if she disclosed about the assault to anyone, they said.