The agency had received sanction to prosecute Shukla, the then Family Welfare Secretary, on November 30 from the Centre after that a charge sheet was filed before special CBI court here today.
Shukla and officials of UP Processing and Construction Cooperative Federation Ltd (PACCFED), including its Managing Director V K Chowdhary, the then Director General of Family Welfare S P Ram, Moradabad based businessman Saurabh Jain, and his firms were booked by the agency in January this year.
While remaining accused were charge sheeted in May this year, the charge sheet against Shukla was pending because CBI was awaiting sanction for his prosecution.
The 55-year-old UP-cadre IAS officer, serving as member Revenue Board, was arrested by the agency in May but was released on bail.
After release, Shukla joined back as member Revenue Board but the UP government issued orders of him being "deemed suspended".
CBI alleged officials of PACCFED favoured ineligible firms and released payment of Rs 16.93 crore on the basis of forged documents.
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In its charge sheet, the agency alleged Shukla along with Ram entered in criminal conspiracy with private firms and gave contract related to upgrading of district hospitals in Uttar Pradesh worth Rs 89 crore on the basis of forged documents.
Out of Rs 16 crore loss caused to exchequer, more than Rs 13 crore was allegedly cornered by Jain, close confidante of former Family Welfare Minister Babu Singh Kushwaha, who used it to bribe public servants and also invested in various companies.