Five other accused are Major (Retd) Ramesh Upadhyay, Ajay Rahirkar, Sudhakar Dwivedi, Sudhakar Chaturvedi and Sameer Kulkarni.
Under the UAPA, 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 who was presiding over the special National Investigation Agency framed the charges against all the accused persons who were present in the court when he read out the charges against them.
All the accused persons pleaded not guilty after framing of charges. The next date of hearing has been set on 2nd November.
The trial in a criminal case commences after the framing of charges.
Six people were killed and over 100 injured when an explosive device strapped on a motorcycle went off near a mosque in Malegaon which is a communally-sensitive textile town in Nashik district of north Maharashtra, on September 29, 2008.
In November 2008, the Anti-Terrorism Squad (ATS) arrested 11 people in this connection. However, in April 2011, the investigation was transferred to the NIA.