The court also ordered that Gujarat cadre IPS officer Satish Verma, who is one of the officers investigating the case, be sent back to the state from June 23.
A division bench of justice Jayant Patel and Abhilasha Kumari told CBI that there was considerable delay in the investigation and filing of the charge sheet resulting in the accused being released on bail.
"This needs to be streamlined and the agency is directed to file the chargesheet in this case by July four so that no other accused gets the benefit of bail due to lapse of time," the bench said.
Commenting on the manner of investigation conducted so far by the investigating agency, the court said CBI needs to concentrate on the genuineness of encounter instead of other aspects like the status of the persons who have lost their lives in the encounter.
"We just want to ensure that the investigation remains on track so that the truth can be unearthed," it said.
On utilisation of services of state cadre IPS officer Satish Verma by CBI, the court said sufficient time was given to CBI to avail the services of Verma.
"We direct that his services to CBI will be available only till June 23 and from the next date, he shall report back to the state government," the court further said.
The court has also ordered CBI to file a compliance report by July 26 when the next hearing of the case is scheduled.
CBI, on the instruction of the High Court, had taken over the probe of the alleged fake encounter in which 19-year-old Ishrat, Javed Sheikh alias Pranesh Pillai, Amjad Ali Rana and Zeeshan Johar were killed on the outskirts of the city on June 15, 2004 allegedly by a state Crime Branch team led by DIG D G Vanzara.