The man and his mother were arrested yesterday, they said.
According to the Nashik rural police, the incident took place on Friday night when the accused, Sachin Shinde, returned home in an inebriated condition and allegedly raped his five-year-old daughter.
Shinde's mother, Anusaya, witnessed the act and anticipating that her son would be arrested for the crime, killed the child by strangling her, Deputy Superintendent of Police (Kalwan division) Devidas Patil said.
She even approached the police and lodged a false complaint, stating that her granddaughter was kidnapped and killed, Patil said.
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During investigation when the police team, along with a dog squad, recovered the body from the spot, the squad led the team to Shinde's house, the officer said.
Based on it, the police grilled the accused and his mother and they confessed to the crime, he said.