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.