Mumbai, June 28: A special NIA court in Mumbai today rejected Sadhvi Pragya Singh Thakur's bail plea in the 2008 Malegaon blasts case and questioned the central agency's probe and its supplementary chargesheet that had absolved her last month.

Judge S.D. Tekale brushed aside the National Investigation Agency's clean chit and its contention that the charges against Pragya were "not maintainable".

"It cannot be said that due to the filing of the further report by the NIA, there is any change in circumstance. If this is the position then merely on the ground that now the NIA has given no objection, it is difficult to accept the prayer (bail) of the applicant," the court said.

The blast had killed eight persons and injured over a hundred in a minority-dominated area in Malegaon, Maharashtra. In 2009, the state's anti-terrorism squad had charged Pragya under the Maharashtra Control of Organised Crime Act (MCOCA) and sections of the Indian Penal Code, saying it was her motorcycle that was used to plant the bomb.

Last month, on May 13, the NIA - the country's top terror probe agency which later took over the case - dropped all charges against her and five others in the supplementary chargesheet it filed, citing lack of evidence.

The NIA also cleared Pragya of the stringent charges pressed against her under the MCOCA and dropped a tough legal provision against the remaining 10 accused, who include a former army officer, Lt Colonel Shrikant Prasad Purohit, drawing allegations of diluting a case involving so-called "saffron terrorists".

Pragya applied for bail on May 30 on the ground that the charges against her had been dropped and that she had had spent a long time in jail since her arrest in 2008.

Then, on June 8, Naseer Bilal, a 64-year-old Malegaon resident, had approached the NIA court requesting it to reject the agency's supplementary charge sheet.

"I had alleged in my application that the second charge sheet of the NIA, the supplementary one, appears to have been influenced by people in power. And that it has been framed to help the accused go scot-free," Bilal, a businessman, who was injured in the 2008 blast, told The Telegraph after Pragya's bail plea was rejected today.

On June 17, Bilal filed another intervention application objecting to Pragya's bail plea. The court had later accepted the application.

The National Investigation Agency had claimed that the evidence against Pragya was weak and the motorcycle, registered in her name, was used by an absconding accused to plant the bomb.

But judge Tekale rejected the NIA's contention.

Pragya's lawyer Prashant Maggu said her client would approach Bombay High Court.