The NIA wanted the court permission to further interrogate the accused Lt Col Prasad Purohit, Sudhakar Udaybhan Dwivedi alias Dayanand Pandey alias Shankaracharya and Major (retd) Ramesh Upadhyaya.
The NIA, which recently took over the investigations from Maharashtra Anti-Terrorism Squad (ATS), had urged the special court, set up under Maharashtra Control of Organised Crime Act (MCOCA), to allow them custodial interrogation of the three accused in connection with the 2008 Malegaon blast case.
According to the chargesheet filed by ATS earlier, Purohit, along with 11 others, had masterminded and carried out a blast in Malegaon on September 29, 2008, in which six persons were killed.
Purohit is the first serving Indian Army officer accused of his involvment in any terror act.
The ATS in a charge sheet filed in 2009 alleged that Purohit and 11 others had planned and executed the blast in Malegaon Sep 29, 2008. The bombing left six people dead.
Purohit, who was serving in Panchmarhi in Madhya Pradesh, was arrested in November that year.
The charges also name him for procuring explosives used in the blast and is one of the founder members of rightwing Hindu group Abhinav Bharat.
Those named in the chargesheet include Sadhvi Pragya, Sameer Kulkarni, and Rakesh Dhavade. Ramji Kalsangra and Sandeep Dange, two more accused, have been declared as absconders.