Former state police chief PC Pande, IPS officers OP Mathur, DG Vanzara, Geetha Johri and Dy SP RK Patel were also named in the chargesheet submitted in the court of judicial magistrate DR Joshi at Danta in Banaskantha district.
The senior IPS officers named in the chargesheet also included two who retired.
The chargesheet, however, was not taken on record by the court due to question of jurisdiction.
The court will decide on the matter after conducting hearing next Monday.
Prajapati, an eye witness in the encounter of Sohrabuddin Sheikh, was killed in a fake encounter allegedly by Gujarat police at Chhapri, in Banaskantha district on Dec 28, 2006.
In a major blow to the ruling BJP, Mr Shah, who was arrested by the CBI in the Sheikh encounter case in 2010, has now been charged in the second fake encounter case of Prajapati for murder, criminal conspiracy, destruction of evidence as also under the provisions of Arms Act.
Mr Shah is out on bail in the Sheikh encounter case but has been barred from entering Gujarat by the Supreme Court.
Former DGP Pande, who was widely criticised for his role as police commissioner of Ahmedabad during the 2002 riots, has also been made accused in the Prajapati case. Mr Pande was the chief of state police when the encounter took place in 2006.
Mr Mathur, retired ADGP who was then (in 2006) heading CID crime and the then IGP CID crime Johri, who was heading the investigation in the Sheikh case, have also been booked as accused in the case.
Mr Mathur currently heads Raksha Shakti University of the state government, while Mr Johri is managing director of Gujarat Police Housing Corporation.
The other two who have been added by the CBI in its chargesheet includes retired DySP Patel, Investigating Officer of Tulsi encounter case and Rajasthan Police inspector Abdul Rehman.
In its chargesheet, the CBI has also retained names of 14 police officers including four IPS officers Vanzara, Rajkumar Pandian, Dinesh MN and Vipul Agarwal, who were earlier made accused in the same case by state CID.