Sudakar Chaturvedi, currently on bail, also alleged that Hindu activists were falsely implicated in the case by the erstwhile Congress-NCP government in a bid to prove the "theory of saffron terror" and for minority appeasement.
"During my questioning, I was asked questions related to my affiliation with the RSS and its chief Mohan Bhagwat. There were specific questions about Yogi Adityanath. They tried to frame him through me," Sudhakr claimed at a press conference in Mumbai.
The blast case was initially probed by the Maharashtra ATS before it was taken over by the NIA.
He and another accused Sudhakar Dwivedi alias Shankaracharya were granted bail by a special NIA court last month. Chaturvedi and others have been accused of attending conspiracy meetings where the terror attack was planned.
Six people were killed and nearly 100 others injured when a bomb strapped to a motorcycle exploded in Malegaon town in Nashik district, about 200 km from Mumbai, on September 29, 2008.
"When I was arrested, the Congress-led UPA government, also comprising the NCP, was in power. We were falsely implicated to appease Muslim voters in a bid to prove the theory of saffron terror," Chaturvedi said.
He alleged that a "lot of hue and cry" was created when Sadhvi Prgaya Singh and Lt. Col. Prasad Purohit were granted bail in the blast case.
While the Sadhvi, accused of plotting the blast, was granted bail by the Bombay High Court in April this year, the Supreme Court granted relief to Purohit in August.
Chaturvedi questioned why no inquiry was ordered against an ATS official who was named by the NIA in its supplementary chargesheet for planting RDX at his residence in Deolali near Nashik.
Chaturvedi said he suspected that an attempt was being made to "save" fugitive underworld don Dawood Ibrahim's brother Iqbal Kaskar, arrested by the Thane Police in an extortion case.
"The arrest of Iqbal Kaskar is a big thing. But not much has been made public about the statements he has given (to police) which raises suspicion that there is an attempt to save him," he claimed.