Bhopal BJP MP Sadhvi Pragya Singh Thakur, Lt Col Prasad Purohit and five others are accused in the case.
A division bench of Justices I A Mahanty and A M Badar granted bail to Dhan Singh, Lokesh Sharma, Manohar Narwaria and Rajendra Chaudhary.
Special NIA Judge V S Padalkar rejected Thakur’s application saying her presence in the court is necessary at this stage.
The criminal jurisprudence in India is based on the presumption of innocence and till a person is actually convicted, he/she is presumed to be innocent.
BJP's Bhopal candidate, an accused in the Malegaon blast, had said that Karkare died because he treated her very badly and earned her curse.
The application was filed by Nisar Sayeed, who lost his son in the blast, a day after the BJP fielded Thakur from the Bhopal Lok Sabha seat against Congress veteran Digvijay Singh.
Sadhvi Pragya candidature: BJP calls Bhopal polls a fight against Congress 'conspiracy' to defame Hinduism
Spokesperson GVL Narasimha Rao claimed that the conspiracy has been "exposed", claiming that Thakur has been discharged in some cases.
In an interim order, a bench of justices A S Oka and A S Gadkari said the special National Investigation Agency (NIA) court should not have passed the order and it was bad in law.
The observations came after NIA repeatedly justified the use of photocopies of some statements of witnesses and confessions of accused persons in the case.
Lt Col Prasad Purohit, an accused in the 2008 Malegaon blast case, today turned hostile while deposing in a court here as a witness in the 2007 Mecca Masjid bomb blast case.
The apex court had last week reserved its verdict on Purohit's plea seeking interim bail in the 2008 Malegaon blast case.