A bench of Justices R.K. Agrawal and A.M. Sapre passed the order on the plea.
On Aug. 17, the Apex Court had reserved its verdict on Lt. Col. Purohit's plea seeking interim bail.
The apex court had on Monday granted bail to him saying it can not deny the relief merely because "sentiments of community was against him". The formalities of furnishing sureties for his regular bail would be completed within a week or two.
The officer, who participated in counter-terrorism operations in Jammu and Kashmir and was also with military intelligence, spent nearly nine years in judicial custody. "It must result in minimum interference with the personal liberty of the accused and the right of the agency to investigate the case", the bench said.
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At the Congress briefing, party spokesperson Manish Tewari said grant of bail was neither a proof of innocence nor guilt as bail was essentially the court's prerogative.
Lt. Colonel Purohit, who was posted with an unit under Southern Command and was an officer from intelligence corp, was suspended from service soon after he was arrested in connection with the Malegaon blast case in in late 2008. He had moved the SC challenging the Bombay High Court's order dismissing his bail plea. The witnesses have been hostile and the cases and charges have been dropped on many people. The High Court had granted relief to another accused in the case, Sadhvi Pragya Singh Thakur, but said that the charges against Purohit were of grave nature.
In its charge sheet, the agency alleged the suspect had selected Malegaon town for the 2008 bombings because of its sizeable Muslim population.
On 28 July, the NIA said there were "several incriminating circumstances" against Purohit, which proved his "deep involvement and complicity" in the 2008 Malegaon blast case, but there was no evidence against Thakur.
The charge sheet had named Sadhvi Pragya Thakur, Lt Col Purohit and co-accused, Swami Dayan and Pandey as the key conspirators.