Special NIA judge V V Patil rejected the bail applications of Manor Singh, Rajendra Chaudhry, Dhan Singh and Lokesh Sharma.
The four accused had urged for liberty after the court discharged eight Muslim co-accused in the case in April.
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The defence lawyers argued that many things which the NIA claimed to have recovered from the accused were easily available in the market.
However, the prosecution argued that there was ample evidence against the accused and the case is very serious in nature. Hence, they should not be given bail.
An explosion had taken place in a bicycle after Friday prayers near Hamidia Mosque near Bada Kabrastan in Malegaon in 2006, killing 37 persons.
The Maharashtra Anti-Terrorism Squad, which first probed the case, had arrested eight Muslim men on the basis of alleged links with the banned Students Islamic Movement of India (SIMI).
Later CBI endorsed it. However, the NIA took over the investigation after Assemanand made revelations in his confession in another case about alleged involvement of Hindu right wing groups in the Malegoan blast case.
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