The high court had on December 18 last year dismissed Lt Colonel Purohit's plea along with that of Sameer Kulkarni, both accused in the 2008 Malegaon blast case.
Lt Colonel Purohit and Mr Kulkarni had told the high court that under the UAPA, the state law and judiciary department, the sanctioning authority, has to seek a report from an appropriate authority.
Lt Colonel Purohit had contended that in his case, the sanction was given in January 2009 but the authority was appointed only in October 2010.
Both Lt Colonel Purohit and Mr Kulkarni are out on bail in the case.
Six persons were killed and 101 injured when an improvised explosive device strapped to a motorcycle went off at Malegaon, a town with sizable Muslim population in north Maharashtra's Nashik district, on September 29, 2008.
On December 27 last year, a special NIA court ruled that Sadhvi Pragya Singh Thakur, Lt Col Prasad Purohit and six others accused in the 2008 Malegaon blast will stand trial on stringent terror charges in the politically-sensitive case that had raised speculation of saffron militancy.
The NIA had earlier given a clean chit to Sadhvi Pragya saying there was not enough evidence against her in the case but the court had rejected the probe agency's submission saying it was difficult to accept the claim, given that her motorcycle was used in the blast.
The accused will face trial now under sections 16 and 18 of the Unlawful Activities Prevention Act (conspiring for and committing/organising a terror act) and under the Indian Penal Code for criminal conspiracy, murder, attempt to murder and causing hurt besides charges under the Explosive Substances Act and Arms Act.
The charges are punishable by various prison terms up to life, and death for murder.
The Anti-Terrorism Squad of the Maharashtra police, which probed the case, had initially charged Thakur, Purohit, Sudhakar Dwivedi, Ramesh Upadhyay, Sudhakar Chaturvedi, Jagdish Mhatre, Rakesh Dhawade, Ajay Rahirkar, Samir Kulkarni, Shyam Sahu, Shivnarayan Kalsangra, Pravin Mutalik and Ramchandra Kalsangra.
Sadhvi Pragya Singh Thakur and Purohit were arrested in the same year with nine others for the blast conspiracy.
On August 21, last year, the apex court had granted bail to Lt Colonel Purohit, who had been languishing in jail for almost nine years for his alleged role in the case, observing there were contradictions in the charge sheets filed by different investigating agencies.