The girl and her mother were allegedly raped by the former minister and his aides. The accused were arrested on the directives of the Supreme Court in March 2017.
The ED has questioned Prajapati about his role in giving three sand mining licences to Shiv Singh and Sukhraj in Fatehpur district.
The woman retracted her statement in court saying that the former minister did not rape her but two of his aides did.
Prajapati, who is under judicial custody in Lucknow Jail in an alleged gangrape case, was recently shifted to Lucknow's King George's Medical College after he complained of illness.
The Samajwadi Party has dismissed allegations that the erstwhile Akhilesh Yadav government had 'shielded' its rape accused minister Gayatri Prajapati.
This development came a day after three persons were detained in connection with the case.