The victim was found lying in a pool of blood on the roof of the sub-inspector's house with wire marks around her neck and it seemed her head had been crushed with a stone, police said.
Victim's father, in his FIR, has alleged that Shailendra had asked the girl to come with him to help in some work while she was at the engagement ceremony, they said.
He raped the girl and then crushed her head with a stone causing her death, they said.
Locals informed that soon after the incident Shailendra and his family left the village in a truck with their belongings, police said.
Agra District Magistrate Zuhail Bin Sagir said action would be taken against Shailendra's father, a panchayat officer, for misleading the police about his son.
Meanwhile the post mortem report of the minor confirmed that rape had been committed on her, police said.