The court granted relief to Vimal Patni, Director of RK Marble, senior IPS officer Narasimha Balasubramaniam and police inspector G Shrinivasan.
The accused have been granted the relief till June 14 after they moved anticipatory bail applications claiming there was no evidence against them.
The special court has now directed CBI to file its reply by June 14.
On March 14, CBI had filed a supplementary chargesheet against former Rajasthan Home Minister Gulabchand Kataria as well as the trio and the local metropolitan magistrate's court had directed them to appear on June 4.
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CBI said Kataria was the person who had introduced Patni to former Gujarat Home Minister Amit Shah.
After coming in contact with Patni, Shah had planned the entire encounter operation with the help of Gujarat police, CBI said.
On September 27 last year, the Supreme Court had ordered the transfer of the Sheikh fake encounter case to Maharashtra after CBI alleged witnesses were being intimidated and the trial could not be held in a free and fair manner in Gujarat.