A bench of justices H L Dattu and C K Prasad stayed the Madhya Pradesh High Court's May 17 order by which the NIA was granted conditional permission to quiz Thakur in presence of her counsel in Bhopal jail where she is presently lodged.
In her petition, she has challenged the NIA's authority to probe the case on the ground that its FIR was lodged before the inception of the agency. Her petition was tagged with the one related to the 2008 Malegaon blast case.
Thakur is also an accused in the Malegaon case and the apex court had restrained the NIA to question other co-accused including Lt Col Shrikant Prasad Purohit and Sudhakar Dhar Dwivedi in that case early this year.
Thakur is accused in five terror cases, including the bombing of the Samjhouta Express and blasts at Ajmer in Rajasthan.
RSS worker Sunil Joshi was murdered in Dewas on December 29, 2007 following which a case was registered against Thakur and others by the Madhya Pradesh police, but the matter was later taken over by the NIA.
Thakur's counsel and senior advocate Basav Prabhu Patil and Anis Gupta challenged the NIA's power to investigate the Joshi murder case contending that the alleged crime was committed prior to NIA Act came into force on December 31, 2008 and the law nowhere specifies that it would be applicable with retrospective effect.
The NIA xourt in Bhopal on April 12 had allowed the agency to interrogate Thakur, which was concurred by the high court but with a condition that her lawyer would be present across a glass partition during Pragya's interrogation.