The plea challenged the investigations done by National Investigation Agency (NIA), a lawyer said.
The notices, returnable Nov 27, were issued Saturday by Maharashtra Control of Organised Crime Act (MCOCA) Special Judge Y D Shinde, said lawyer J P Mishra, representing one of the accused.
A powerful blast took place near a mosque in Malegaon, Nashik on September 8, 2006, killing 37 people and injuring over 160.
The police and subsequently, ATS investigations led to the arrest of nine Muslim youth for their alleged involvement in the terror incident.
Thirty-seven people were killed in the blast in Malegaon in September 2008
Manohar Singh, an accused, has challenged the fairness of the NIA probe which enabled the nine Muslim youth who had been earlier arrested in the terror case, to get bail.
The Muslim youth had later contended that they were framed in the terror case by the ATS and CBI and the investigations by NIA revealed that they were innocent.
Mishra said the NIA negated the investigations of ATS and CBI and hence, Manohar Singh has made an application in the matter of fairness of the NIA probe.
Opposing Manohar Singh's application, the Jamiat Ulema-E-Hind, which is defending the nine accused Muslim youth, contended that it was meant to misguide the court to prolong the hearing of the discharge applications.
"Manohar Singh has no locus standi and hence his application is not maintainable under law and liable to rejected without giving any opportunity to ATS and CBI to give any excuse justifying their deliberately false charge-sheet against the nine Muslim youth," Jamiat Ulema-E-Hind lawyer Sharif Sheikh said.
In December 2006, the case was taken over by the Central Bureau of Investigation which endorsed the probe by the ATS.
The case took a turn in 2010, when Swami Aseemananda was arrested by the CBI and he gave a confessional pointing to the involvement of certain right-wing Hindu fanatics in a second terror blast in 2008 in the Muslim majority town of Malegaon.
Following the sensational revelations, the NIA stepped into the picture, further probing the 2006 Malegaon blast case and made four new arrests - Manohar Singh, Dhan Singh, Lokesh Sharma and Rajendra Choudhary, while one more accused Ramji Kalsangra was shown as absconder.
Last year, the Muslim youth were granted bail and a couple of months ago, they moved the court seeking discharge from the 2006 Malegaon blast in view of the NIA investigation outcome.