The NIA filed the charge sheet in a special court in Mumbai in which the probe agency has named Kalsangra alias Ramji, a key suspect, Dhan Singh, Rajendra Chaudhary and Manohar (already in custody).
The four have been charged with murder and other sections of Indian Penal Code and Explosives Act.
The move by NIA has left Mumbai Police's elite Anti Terror Squad, which had arrested nine Muslim youths for allegedly conspiring and triggering explosion in the powerloom township located 290 kms from Mumbai, and the CBI red faced.
41-year-old Kalsangra, who has been declared as a proclaimed offender and also carries a cash reward of Rs 10 lakh, is alleged to be the main planner as well as the person who had strapped the cycles with explosives which were planted outside a mosque on September 8, 2006.
The agency made its breakthrough in this blast case when it arrested Chaudhary, Dhan Singh and Manmohan, who were alleged to be a part of the criminal conspiracy and touted as planter of explosives in communally-sensitive Malegaon township.