The NIA has named Lokesh Sharma, Dhan Singh, Rajendra Chaudhary and Manohar Narwaria in its chargesheet.
The multiple bomb explosions in Malegaon, a communally-sensitive town in Nashik district of Maharashtra, had occurred near a mosque on September 8, 2006, killing 37 people and injuring over 100.
After the explosions, Maharashtra Anti-Terrorism Squad (ATS) had arrested nine suspects.
However, the Maharashtra Control of Organised Crime Act (MCOCA) court later granted them bail after new details emerged about the bombings.
The probe into the blasts was handed over to CBI which endorsed the ATS' findings. The case went to NIA, which came into existence in 2009 following 26/11 Mumbai attacks.
The NIA cracked the case with the arrest of six activists of the right-wing Hindu groups. Lokesh Sharma and Devender Gupta, former members of Rashtriya Swayamsevak Sangh (RSS), were the first to be arrested in the case.
Two others, Sandeep V Dange and Ramchandra Kalsangra, are absconding. According to the investigators another key accused Sunil Joshi was gunned down by his associates in December 2007 following some differences.
Malegaon had seen another terror attack in 2008 allegedly by right-wing Hindu groups. Sadhvi Pragya Singh Thakur and former Lt Col Srikanth Purohit were arrested in connection with the incident.