The investigators had earlier arrested nine Muslim men, however the NIA, after it took over the probe, found that the blast was the handiwork of a Hindu extremist organization.
In its application filed this week before the Maharashtra Control of Organised Crime Act Court's judge Y D Shinde, NIA has said the accused Manohar Singh has no right to be heard (locus standi) in this issue.
"As per provisions of law, co-accused has no locus standi in the discharge application filed by any other accused," NIA has said.
The Maharashtra Anti-Terrorism Squad had arrested Noorul Huda Samsudoha (28), Shabbir Ahmed Masiullah (41), Raees Ahmed Rajab Ali Mansuri (35), Dr Salman Farsi Abdul Latif Aimi (40), Dr Farogh Iqbal Ahmed Magdumi (38), Mohammad Ali Alam Sheikh (42), Asif Khan Bashir Khan alias Junaid (35), Mohammad Zahid Abdul Majid Ansari (31) and Abrar Ahmed Gulam Ahmed (38) in connection with the two blasts.
But NIA claimed that the blasts were carried out by a Hindu right-wing group, and arrested Lokesh Sharma, Dhan Singh, Manohar Singh and Rajendra Choudhary. They were charged.
The aforesaid nine Muslim men got bail, and filed application for discharge, which is being heard.
The Hindu group came under the scanner following a confession of Swami Aseemanand, an accused in the 2007 Mecca Masjid blast case.
Two blasts in Malegaon, a communally sensitive town in Nashik district, killed 37 people on September 8, 2006.