Mr Purohit and six others, including BJP MP Pragya Singh Thakur, are facing trial in the case.
The Supreme Court has junked a plea filed by Lieutenant Colonel Prasad Shrikant Purohit seeking discharge in the 2008 Malegaon blast case.
Mr Purohit had moved the top court challenging the January 2 order of the Bombay High Court rejecting his appeal.
Mr Purohit and six others, including BJP MP Pragya Singh Thakur, are facing trial in the case. All the accused are currently out on bail.
A bench of Justices Hrishikesh Roy and Manoj Misra refused to interfere with the high court order.
"The challenge here is to the order of the High Court whereby it was observed that sanction is not needed under Section 197(2) of the CrPC for the prosecution of the petitioner as his impugned conduct do not pertain to any of his official duties.
"Having noted the basis of the impugned judgment, we see no reason to interfere with the same and accordingly, the Special Leave Petition is not entertained," the bench said.
The top court, however, clarified that the trial court should not be influenced by observations in the high court's order.
"The observation made in the impugned order for the purpose of examining the issue of sanction should not prejudice either the prosecution or the defence, in the proceedings before the trial court," the bench said.
Among other grounds for seeking discharge, Mr Purohit had claimed lack of sanction under relevant provisions of the Code of Criminal Procedure (CrPC) to prosecute him.
On September 29, 2008, six people were killed and more than 100 injured when an explosive device strapped to a motorcycle went off near a mosque in Malegaon, a communally sensitive town in Maharashtra's Nashik district.
According to the Maharashtra Police that conducted an initial probe into the case, the motorbike to which the explosive was strapped was registered in Pragya Thakur's name, which led to her arrest.
The National Investigation Agency later took over the probe into the case.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)