The panel included KH Kurlekar, who was Deputy Superintendent of Yerwada prison at the time, JM Kurkarni, an inspector of CID Pune, Rashmi Joshi, a member of Dakshata Sameeti, and NGO Greenlife Foundation.
In the report submitted in 2015, the panel said Pragya's allegations couldn't be substantiated through evidence.
The Commission collected proofs from jail, courts and the hospital where she was admitted.
Before the panel, SC also spoke about her allegations
Saying the allegations didn't need further probe, the panel closed the case.
Notably, in 2011, the Supreme Court also made a brief reference to Pragya's allegations. She had claimed in 2008 that ATS forced her aide Bhim Pasricha to thrash her.
But the division bench of Justices JM Panchal and HL Gokhale found the claims flimsy. They said doctors of two hospitals didn't find any injury marks.
SC also added that Pragya wasn't detained illegally
The top court also noted that Pragya was produced twice before the Nashik court (on October 24 and November 3) but she didn't mention any such incident.
On Pragya's allegations that she was illegally detained, SC relied on Bombay High Court's findings of 2010.
"Not once were the applicant's movements restricted, nor was she confined to the ATS office after interrogation," HC had noted.
Meanwhile, PM Modi defended Pragya, said she was ill-treated
He expressed displeasure that a sadhvi was treated this way and said her candidature would cost Congress dearly.
Notably, Pragya hasn't been acquitted and still faces trial under various sections of Unlawful Activities Prevention Act (UAPA). Only charges under Maharashtra Control of Organised Crime Act (MCOCA) have been dropped.