Special judge of a Protection of Children from Sexual Offences (POCSO) court Om Prakash Mishra granted bail to Prajapati, Vikas Verma and Amrendra Singh alias Mintu.
The court asked Prajapati to furnish two sureties of Rs 1 lakh each and a personal bond of the same amount.
It held that the complainant had given her implied consent in the incident.
The court observed that since she did not complain to the police or the competent court despite claiming that they had been committing rape on her for last three years, it was an indication that she had given implied consent.
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Prajapati (49) was then a minister in the Akhilesh Yadav- led Samajwadi Party government in Uttar Pradesh.
When asked about the bail granted to his former cabinet colleague, Akhilesh said, "It's good that he got bail. Please tell me if there is anything wrong in it."
After being on the run for nearly a month, Prajapati (49) was arrested from the Aashiyana area here on March 15 and was sent to jail for allegedly raping a woman and attempting to rape her minor daughter in 2014.
Prajapati had approached the Supreme Court to get a stay on his arrest.
But the apex court asked him to approach the court concerned.
At the time of his arrest, Prajapati had claimed that he was innocent and the charges were a conspiracy to malign him.
The former minister had said that he was prepared for a narco test to bring out the truth and also demanded a similar test on the minor victim.
The allegations against Prajapati were raked by the BJP during the state assembly elections to attack the then Akhilesh government.
The BJP had accused Akhilesh of shielding his tainted minister, a charge refuted by the Samajwadi Party.