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.
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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