The plea, filed by the father of one of the blast victims, came up for hearing before a bench headed by Justice A M Khanwilkar.
Malegaon case: Bombay HC adjourns hearing in discharge plea of BJP MP Pragya Singh Thakur till November 18
The accused have also challenged the Unlawful Activities Prevention Act sanction for prosecution.
Special NIA Judge V S Padalkar said conducting the trial in a 'transparent manner' was among the reasons for rejecting the NIA's plea.
She was addressing a condolence meeting at the state BJP office to pay tributes to Jaitley and former Madhya Pradesh chief minister Babulal Gaur.
Bhopal BJP MP Sadhvi Pragya Singh Thakur, Lt Col Prasad Purohit and five others are accused in the case.
A division bench of Justices Indrajit Mahanty and Riyaz Chagla was hearing a petition filed by Purohit challenging the sanction granted to prosecute him under the UAPA Act.
The court asked NIA advocate Sandesh Patil to inform within two weeks till what time the trial is expected to go on and give a schedule, stating by when it will be completed.
Two motorbikes and five cycles seized from the blast site were brought in a tempo to the sessions court in South Mumbai for examination by special NIA Judge Vinod Padalkar.
Mayawati accused poll panel of lacking probity and acting with zero objectively, on the other the BSP chief held PM responsible for the alleged ‘fall in the integrity of country’s institutions.
Lt Col Prasad Purohit, an accused in the 2008 Malegaon blast case, today turned hostile while deposing in a court here as a witness in the 2007 Mecca Masjid bomb blast case.
AIMIM chief Asaduddin Owaisi on Monday accused the Modi government of "going soft" on terror cases after the Supreme Court granted bail to the main accused in the 2008 Malegaon blasts.
The apex court had last week reserved its verdict on Purohit's plea seeking interim bail in the 2008 Malegaon blast case.
The HC had refused to accept Purohit's contention that he had attended the meetings as part of a "covert military intelligence operation."