Prajapati, a key witness to the November 2005 killing of Sohrabuddin Sheikh and his wife Kausarbi, was gunned down by police on December 28, 2006 near Chhapri village, around 7 km from Ambaji.
The CBI had earlier conducted a similar reconstruction and to plug the loopholes in the first one carried out the second one. The encounter case is monitored by the Supreme Court.
The CBI team, led by joint director V Lakshminarayana, along with the AIIMS team and the forensic experts arrived at the village in the morning hours, CBI sources said.
"The experts obtained crucial data such as the distance between the police vehicle and the car in which Prajapati was travelling; location of Prajapati's body after the encounter as mentioned by CID and regarding how police officers fired at Prajapati and the distance from which they fired," they said.
"They also video recorded the reconstruction," sources said.
The supreme court had transferred the case to the central agency on April 8, 2011 with a direction to complete the probe within six months. However, the apex court granted the fourth extension to CBI setting June 30 as the deadline for filing the chargesheet.
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The Prajapati encounter was earlier probed by the state CID which had registered an 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.