Thakur moved the high court after the special court for Maharashtra Control of Organised Crime Act cases denied her bail on June 28.
The division bench of justices N H Patil and P D Naik asked the NIA to submit a compilation of all the previous orders and judgements pertaining to the case.
Thakur was given a clean chit by the NIA earlier this year, but the trial court refused her bail.
In November 2015, the special court denied her bail, holding that prima facie there was some evidence against her.
But in May, NIA filed a fresh charge sheet (after taking over the case from Maharashtra ATS), which gave a clean chit to Thakur.
Her lawyer, advocate Jai Prakash Mishra, argued today that there was no material evidence against her. NIA's lawyer also told the high court that the agency had concluded that charges against her could not be substantiated, and the earlier charge sheet filed by ATS was erroneous.
Six persons died and 100 were injured in the bomb blast at Malegaon, a predominantly Muslim town in north Maharashtra, on September 29, 2008.
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