CBI IG, P Kandaswamy, who is heading the investigation team, confirmed that FIR had been filed. He, however, declined to divulge more details.
The Supreme Court, on April 8, had ordered that the probe into Prajapati's killing be transferred to the CBI, following the appeal filed by his mother, Narmada Bai, alleging that her son was killed in a fake encounter by the Gujarat police as he was a key eyewitness in the November 2005 killing of Sohrabuddin Sheikh.
Prajapati, a close aide of Sohrabuddin, an alleged gangster, was killed in an encounter near Chapri village in Banaskantha district on December 28, 2006.
The court had also criticised the tardy investigation by the Gujarat police. The Supreme Court bench regretted that the State police took more than three-and-a-half years to file the charge sheet.
The Prajapati encounter was being probed earlier by the state CID which had registered FIR last year in Ambaji police station. Seven policemen including IPS officer Vipul Agarwal were arrested in the case.
Three suspended IPS officers, D G Vanzara, Rajkumar Pandiyan and Dinesh M N, who are accused in the Sohrabuddin encounter case, have been shown as accused in the Prajapati case too, by the CID.
The apex court, while passing the order, had taken into consideration the CBI's argument that Prajapati's case was crucial for unearthing the "larger conspiracy" in the Sohrabuddin case.
The court had observed that both oral and documentary evidence raise strong suspicion that Prajapati's encounter was fake and stage-managed, as predicted by the deceased in a number of communications.
Observing that there was a connection between the two encounters, apex court had said that there was substantial material on record which makes it probable that the prime motive for eliminating Prajapati was that he was a witness to abduction of Sohrabuddin and Kausar Bi.
Gujarat government, during the arguments, had strongly opposed CBI probe on the ground that Prajapati's case was in no way connected to the encounter of Sohrabuddin Sheikh.