Mumbai, June 28: A special NIA court in Mumbai today rejected Sadhvi Pragya Singh Thakur's bail plea in the 2008 Malegaon blast 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, 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 Col 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 spent a long time in jail since her arrest in 2008.

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

"I had alleged in my application that the second chargesheet 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 NIA 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. At this stage, prima facie, the court said, Pragya "can't avoid her connection with the vehicle" as it was "registered in her name".

The court also dwelt on Pragya's participation in a meeting in Bhopal where the alleged conspiracy was hatched. The judge said a "safe conclusion" could be drawn that "there was discussion about jihadi activities in Aurangabad and Malegaon".

"There was also a discussion on preventing and stopping these activities. The participants in the meeting, including (the) accused (Pragya) wanted to establish Hindu Rashtra. This was made clear from witness statements," the judge said.

On the possible motive, the court said details of the meeting and discussions show they wanted to "overawe the government (of the day) and... establish a government in exile".

Reading from a 20-page order, the judge also said the NIA's claim that Pragya couldn't be tried under the MCOACA because of lack of evidence was not acceptable as the Supreme Court had earlier made it clear that the tough law did apply against her and her alleged accomplices.

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

A retired NIA official who requested anonymity said: "The court's observation is a big blow to the NIA's chargesheet in the case and it raises a big question mark on the quality of investigation."

Senior NIA officials refused to comment.

Minister of state for home Kiren Rijiju said: "It is between the court and the probe agency and the government has nothing to say on this."

This is not the first time the NIA has been accused of weakening the case since the Narendra Modi government came to power in May 2014. Public prosecutor Rohini Salian had quit last year alleging pressure from a senior official to "go soft" on the accused.

After the NIA's clean chit to Pragya last month, the Congress had accused NIA director Sharad Kumar of weakening the terror case to "protect the RSS brass" and demanded his resignation. Kumar was given a year's extension after his retirement last year.