The chargesheet, running into five volumes, was filed in a Maharashtra Control of Organised Crime Act (MCOCA) Court of Special Judge Prithviraj Chavan.
Ramji Kalsangra has been shown as absconding accused in the chargesheet. The bombings were part of a series of explosions that had taken place on September 8, 2006, in Malegaon, a communally-sensitive town in Nashik district of Maharashtra, located about 300 kms from Mumbai.
The explosions, which caused the death of 37 people and injured over 125, had taken place in a Muslim cemetery, adjacent to a mosque, at around 1.15 pm after the Friday prayers on the Shab-e-Baraat, a holy day.
Most of the blast victims were Muslim pilgrims. According to police, two bombs attached to bicycles had exploded, triggering a stampede.
After the blasts, the Maharashtra Anti-Terrorism Squad had arrested nine suspects. However, the MCOCA court had granted bail to all of them in November 2012.
The probe into the blast was handed over to the Central Bureau of Investigation which endorsed the ATS findings.
The case then went to the NIA, which came into existence in 2009. Malegaon had seen another terror act in 2008 allegedly by right wing Hindu groups and Sadhvi Pragya Singh and former Lt Col Srikant Purohit were arrested in connection with it.