Patil, 28, stayed next to the room of the Sanstha founder Jayant Balaji Athwale, it said.
"Malgonda Patil was an active member of Sanatan Sanstha involved in the publicity of Sanstha and used to hold satsang (meetings) at various places. He stayed in Abhyasika/ Sant Kakshay of Sanatan Sanstha Ashram building in Ponda," the NIA said in its chargesheet.
Right-wing Hindu organisation, Sanatan Sanstha, had initially distanced itself from all the accused in the Margao blast.
NIA filed the chargesheet on May 17 in south Goa district court. Malgonda Patil, who died while ferrying the explosives in Margao, was the Managing Trustee of Dharma Prachar Sabha, a trust of Sanatan Sanstha.
The investigating agency also found that Malgonda Patil and another accused Dhananjay Ashtekar hatched the blast conspiracy at the former's room, which was close to the room of Jayant Balaji Athawle on the Ashram's first floor during June 2009, four months before the blast.
Investigators have found that Margao blast was just a loop in the serial blast planned at five different places across Goa on October 16, 2009.