CBI sources said the charge sheet was filed against Shukla, the IAS topper of the 1981 batch, and Kushwaha under charges of corruption and cheating at a special court in Ghaziabad.
Shukla was also the mission director of the National Rural Health Mission in Uttar Pradesh.
They said the charges were not filed against accused R P Jaiswal as he had passed away during the course of investigation.
The first charge sheet was filed in the case on February 25, 2013.
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The case pertains to alleged irregularities in the supply of 515 "first referral unit" kits and 2,050 "intra-uterine" device kids worth Rs 31.59 crore under the NRHM.
The UPA government had launched NRHM in 2005-06 in various states for providing better medical facilities to all citizens and vulnerable sections of the population.
The accused caused a loss of Rs 21.20 crore and made illegal gains in the process of implementing the scheme, the charge sheet has alleged.
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