The High Court has ruled that the charges - including criminal conspiracy and murder - will apply against Mr Pande, who had appealed for them to be dropped on account of lack of evidence. Mr Pande is currently the Additional Director General of Police.
In 2004, he was the head of Ahmedabad's Crime Branch, when its top officers shot dead Ishrat, a 19-year-old college student from Mumbai, along with three other people on the outskirts of the city. The police said it had been told by the Intelligence Bureau that the group was operating on behalf of terror group Lashkar-e-Taiba to assassinate Chief Minister Narendra Modi.
A Special Investigation Team appointed by the Gujarat High Court said that was untrue.
Mr Pande was declared an absconder by the CBI court in Ahmedabad on June 21.
The CBI's chargesheet, in which it will list the accused and outline the evidence against them, is to be filed on Thursday in the High Court.
Mr Pande had claimed in his petition that he passed on intelligence inputs to his force and that he did not play a larger role in the fake encounter.
However, the CBI has in court described him as "the mastermind."
"He received inputs, passed it to his subordinates and arranged everything... In fact, he was in total control of the operation. He actually acted as Rambo," Additional Solicitor General Indira Jaising had alleged.