In her petition, Sadhvi has sought the court to quash an order passed in April last year transferring investigations into the blast case to the NIA by the Union government.
According to her plea, the central government cannot transfer investigations of a case without concurrence from the state government.
A division bench of Justices A S Oka and S S Shinde, however, said the petitioner will have to satisfy the court on whether an accused has the right under law to challenge transfer of investigations. "What is the locus of the accused," the court said.
The bench has directed the Union government to file its reply by February 4, 2013.
"NIA does not have retrospective power to re-investigate into those offences where charge sheet has been already filed by state investigating agencies," Sadhvi has said in her petition adding the agency has a political agenda.
Sadhvi and more than ten others, members of right wing organisation Abhinav Bharat, were arrested for their alleged involvement in the September 2008 Malegaon blast case.