In its charge sheet filed before the special judicial magistrate here, the agency has alleged that shooters Anand Prakash Tiwari and Vinod Sharma had murdered the then CMOs Dr VK Arya and BP Singh.
The agency has also named one Ram Krishna Verma, who had allegedly hired them to murder the CMOs who grew suspicious about the alleged corruption in the NRHM schemes here and started probing them, CBI sources said.
According to the CBI, the alleged motive behind the murder was the fear of being exposed in misappropriation of funds in the National Rural Health Mission (NRHM).
The agency had also recently arrested former CMO AK Shukla in connection with the murder case of Arya on charges of criminal conspiracy.
There were indications emerging that Shukla could also be allegedly involved in killing of another Chief Medical Officer BP Singh, the sources said.
Arya was murdered while he was taking a morning walk on October 2010 at Vikas Nagar area while Singh was shot dead in April last year at Gomti Nagar.
Shukla was earlier arrested by the CBI last year in connection with the NRHM scam but was granted bail by the Allahabad High Court.
The court had on July 27 directed the CBI to probe the murders of the two CMOs and also irregularities in implementation of the NRHM.