Under the Unlawful Activities Prevention Act and several sections the accused have been charged with being part of a terrorist act, and under IPC they have been charged with criminal conspiracy and murder.
Judge Vinod Padalkar, presiding over the special National Investigation Agency court, framed charges against the accused persons.
The court set November 2 as the next date of hearing.
The other five accused in the case are Major (retd) Ramesh Upadhyay, Sameer Kulkarni, Ajay Rahirkar, Sudhakar Dwivedi and Sudhakar Chaturvedi.
All the accused were present in the court when the judge read out the charges against them.
Six persons were killed and over a 100 were injured when an explosive device strapped on a motorcycle went off near a mosque in Malegaon, a town located about 200 km from Mumbai in North Maharashtra, on September 29, 2008.