On a complaint filed by activist and advocate Nutan Thakur, Prajapati was under the Lokayukta scanner for corruption in illegal mining.
[1] Later Nutan Thakur's husband ex IPS officer and Present, Adhikar Sena alleged that ex Uttar Pradesh Chief Minister Mulayam Singh Yadav threatened him for his wife's Lokayukta case against Prajapati.
[3] On 17 February 2017, the Supreme Court of India directed Uttar Pradesh police to lodge a complaint in connection with a rape case.
[4] In 2016 Allahabad High Court charged him with allowing illegal mining in his capacity of mining minister in Shamli, Hamirpur, Fatehpur, Siddharthnagar, Deoria, Kaushambi and Saharanpur - in violation of rules and ban by the National Green Tribunal.
The woman then approached Supreme Court, which directed the police to lodge a report.