Those against whom the charge sheet was filed for murder and criminal conspiracy include absconding Additional DGP PP Pandey and suspended DIG DG Vanzara.
"The encounter was a joint operation between Gujarat police and Subsidiary Intelligence Bureau (SIB) of the state," CBI said in the charge sheet, adding, "the encounter was fake".
The CBI told the court of Additional Chief Judicial Magistrate HS Khutwad that their investigation has established offence against all seven police officers charge sheeted in the case.
The investigation is going on against four Intelligence Bureau officers, including its Special Director Rajinder Kumar, and three other officers - P Mittal, M K Sinha and Rajiv Wankhede, it said.
Supplementary charge sheet would be filed against IB officers once the investigation was over, the court was told.
Apart from Pandey and Vanzara, other Gujarat police officers who have been charge-sheeted are GL Singhal, Tarun Barot, NK Amin, JG Parmar and Anaju Chaudhary.
Ishrat, hailing from Mumbra in Thane district adjoining Mumbai, Javed Shaikh alias Pranesh Pillai, Amjadali Akbarali Rana and Zeeshan Johar were killed in the encounter with the Gujarat police on the outskirts of Ahmedabad on June 15, 2004.