Special judge J K Pandya exempted Amin to mark his presence before the court every Thursday, which was one of the conditions that the court had imposed on him while granting bail in May 2015.
The court, however, asked him to to remain present during the trial.
Seeking exemption from weekly appearance, Amin had argued before the court that there was no complaint against him regarding intimidation or influencing of witnesses or any such thing that could hamper investigation.
Amin had served eight years in jail following his arrest in August 2007.
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He had recently decided to step down as an officer of Gujarat Police to which he was reinstated by the state government after getting bail.
He had resigned from his post along with co-accused Tarun Barot on a petition challenging their reinstatement.
Amin had also faced trial in the Sohrabuddin Sheikh encounter case but was discharged last year by a special CBI court in Mumbai.
The crime branch had then claimed that those four were Lashker-e-Taiba (LeT) operatives and had landed in Gujarat to kill the then chief minister Narendra Modi.
According to CBI's charge-sheet in 2012, it was a fake encounter orchestrated jointly by Gujarat Police and Intelligence Bureau.
Singhal, Barot, Chaudhari and Parmar secured default bail as the probe agency could not file charge sheet against them in the stipulated time period of 90 days after their arrest.
According to the charge sheet, Amin had fired five bullets at Ishrat and three others.