The apex court also listed the plea of co-accused Shrikant Purohit seeking bail for hearing on August 14 along with the Thakur case.
"Both matters are on similar facts," a bench comprising Justices R K Agarwal and M M Shantanagoudar said.
The court's remarks came when senior advocate Harish Salve, appearing for Purohit, sought to know why the case was being adjourned.
The National Investigating Agency (NIA) had filed its reply in the case of Purohit saying there was ample evidence against him, but no evidence against Thakur.
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"The high court failed to appreciate that Sadhvi Pragya Singh Thakur is an influential person and is likely to wield her power and influence in an illegal and unlawful manner to tamper with evidence and influence witnesses," he has said.
It has said that she had been denied bail by a special court in Mumbai several times in the years 2011, 2012, 2015 and 2016 on the ground that "a prima facie case is clearly made out against her".
Thakur was granted bail by the high court, which, however, had refused a similar relief to Purohit.
On other hand, the apex court had on May 5 sought response from the NIA and the Maharashtra government on the plea of Purohit seeking bail.
A special MCOCA (Maharashtra Control of Organised Crime Act) court had earlier ruled that the Anti-Terrorist Squad had wrongly applied the MCOCA against Thakur, Purohit and nine others.
The 4,000-page charge sheet had alleged that Malegaon was selected as the blast target because of a sizeable Muslim population there.
It named Thakur, Purohit and co-accused, Swami Dayanand Pandey as the key conspirators.
The charge sheet had alleged it was Pandey who had instructed Purohit to arrange explosive RDX, while Thakur owned the motorcycle which was used in the blast.
Rakesh Dhawde, Ramesh Upadhyay, Shyamlal Sahu, Shivnarain Kalsangra, Sudhakar Chaturvedi, Jagdish Mhatre and Sameer Kulkarni were the other accused.
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