The organisations in question are Dharma Prachar Sabha and Hindu Dharma Prathisthan.
Patil's link to the two organizations were confirmed in the home ministry report presented during the state assembly session on Dec 16.
Home Minister Ravi Naik said that the gelatin sticks, detonators and timer circuits were used to trigger off the blasts.
Patil was linked to the Hindu organisation Sanatan Sanstha prior to latest revelation.
Malgonda Patil and Yogesh Pati, the two accused behind the Margao blast died in the blast as the bomb exploded prematurely.
As per the home ministry's directives, the case will be handed over to the National Investigation Agency (NIA).