The agency has alleged that cops at the Ahmedabad crime branch had written the FIR even before the "fake encounter" took place. It has charged seven policemen - including DG Vanzara who is in jail and then crime branch chief PP Pande, who is absconding - with murder, conspiracy and destruction of evidence, abduction and under sections of the Arms Act.
The chargesheet says the CBI suspects the involvement of senior intelligence officer Rajendra Kumar and his role and that of others in the IB needs to be investigated further.
The chargesheet rebuts the Gujarat Police claim that Ishrat, a Mumbai college student, and the three men shot dead along with her, were driving towards Ahmedabad when they were intercepted and killed in an exchange of fire on June 15, 2004. The chargesheet says they were abducted and that a cop drove a car with three of them to the encounter site.
It alleges that one of the men killed in the encounter, Zeeshan Ali, was abducted by the police in April that year, another, Amjad Ali, in May and that Ishrat and a third man Javed were abducted in June. The CBI chargesheet says they were held at different farmhouses.
The agency has alleged that the weapons found with Ishrat and the others at the encounter site were supplied by the state Intelligence Bureau.
Rajendra Kumar was the Gujarat station chief of the Intelligence Bureau or IB when Ishrat and the others were shot dead; the policemen involved said they had received alerts from the IB that the group planned to assassinate Chief Minister Narendra Modi on behalf of terror group Lashkar-e-Taiba.
Mr Kumar's interrogation by the CBI has created a sharp divide between his agency and the CBI, which is expected to name him as an accused in its next chargesheet, to be filed most likely after he retires at the end of July.
The IB official has said that though he shared information with the police about the possibility of Ishrat and the others being terrorists, he did not sanction the encounter. The CBI, however, says it has testimony from eyewitnesses and other evidence that will later show how Mr Kumar played a key role in the killings and in what it calls a larger conspiracy.
The chargesheet does not go into whether Ishrat and the others were terrorists, as the Gujarat Police alleges. The CBI, which took over the case in 2011, has been asked by the Gujarat High Court to establish whether this was a fake encounter and not whether Ishrat and the others were terrorists or not.
The CBI has said a supplementary chargesheet will be filed in a month.