A Supreme Court bench comprising Justices J Chelameswar and A M Sapre, on 11 September, asked NIA and central government to file their response in a week to a plea alleging the government of going soft on the accused in the 2008 Malegaon blasts case.
The plea challenges removal of Special Public Prosecutor (SPP) and alleges that the government has been pressurising her.
The bench, however, did not allow the submission of senior advocates Kapil Sibal and Indira Jaising that hearing on the bail applications of the accused persons be stayed for the time being.
The bench has also issued notice to Maharashtra government in the case.
Earlier, a Supreme Court Judge had recused from hearing the plea, saying that he had represented certain accused in the matter.
The PIL, filed by social activist Harsh Mander, has accused NDA government of trying to interfere with the functioning of the prosecutor in the case by exerting "pressure" on her to "go soft" on the accused. It alleged that the executive was attempting to influence the judicial system.
It has alleged that NIA officials had pressured erstwhile Special Public Prosecutor in case, Rohini Salian, "presumably" under instructions from their "political masters".
Salian, who was SPP in the case, had alleged that an NIA officer had told her to go soft on the accused. She also claimed the same officer had told her that she would be replaced. Salian is no longer on NIA's panel of lawyers.
The petition has sought the apex court's intervention to ensure a fair trial as there were reasons to "credibly fear" that "executive is attempting to influence the judicial system to cave in to the pressure exerted by it in all matters, including affording protection to right-wing extremists who sympathize with its ideology".
The 4,000-page charge sheet had alleged that Malegaon was selected for the blasts because of its sizeable Muslim population. It named Pragya Singh Thakur, Purohit and another accused, Swami Dayanand Pandey, as the key conspirators.
The charge sheet had alleged it was Pandey who had instructed Purohit to arrange for RDX, while Pragya owned the motorcycle which was used in the blast.
Ajay Rahirkar, another accused, allegedly organised funds for the terror act, while conspiracy meetings were held at Bhonsala Military School in Nasik, according to charge sheet.
Rakesh Dhawde, Ramesh Upadhyay, Shyamlal Sahu, Shivnarain Kalsangra, Sudhakar Chaturvedi, Jagdish Mhatre and Sameer Kulkarni were the other accused.
The blast on September 29, 2008 had left four dead and nearly 80 injured.