The girl in her statement, said her father, Rakesh, was sexually abusing her for the past one month.
The girl's mother registered a case against Rakesh Tuesday evening.
Rakesh is missing and on the run, a police officer said Wednesday.
The family lives in Patel Nagar in west Delhi.
"The girl told her mother about the incident Friday and the mother approached to the police with her family members," said the officer.
Rakesh also had an illicit affair with his sister-in-law, the girl said in her statement.
Photos: Aamir Khan with 'Dangal' actresses at fashion show
Spotted: Twinkle Khanna, Shriya Saran at an event in Mumbai
Andrew Flintoff's birthday: 10 players who entered different sports
Photos: Ranveer Singh and Vaani Kapoor go 'Befikre'
Photos: Aishwarya, Sridevi, Karisma at Manish Malhotra's birthday bash