During investigation, "sufficient evidences have not been found against" Pragya Singh Thakur and five others, the NIA said, adding it has submitted in the charge sheet "that the prosecution against them is not maintainable".
Seven people were killed in the blast when they were coming out of prayers during Ramzan on September 29, 2008.
There have been a lot of twists and turns in the probe into the Malegaon blast which was described as a handiwork of people associated with Hindu right wing groups.
Purohit and Pragya had moved several applications before Bombay High Court and Supreme Court challenging the charge sheet and applicability of stringent Maharashtra Control of Organised Crime Act (MCOCA) in the case.
Shiv Narayan Kalsangra, Shyam Bhavarlal Sahu, Praveen Takkalki, Lokesh Sharma and Dhan Singh Choudhury are the other five accused against whom charges have been dropped besides Sadhvi.
"In furtherance of same, the confessional statements recorded under provisions of MCOCA by ATS Mumbai have not been relied upon by the NIA in submitting the present final report," the agency said in its charge sheet.
Lt Col Purohit and nine others will now be tried for charges including murder and conspiracy under the provisions of anti-terror law UAPA, IPC, Arms Act and Explosives Substance Act.
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