A special NIA court on Tuesday rejected the bail application of 2008 Malegoan blast accused Sadhvi Pragya Singh Thakur who had been given a clean chit by the probe agency last month.
The National Investigation Agency (NIA) had also not opposed her bail application.
Special Judge S D Tekale rejected the bail plea in an in-camera hearing.
In her application, Pragya had contended that there was no evidence against her.
Though the motorcycle used in the blast was owned by her, according to one of the witnesses, it was in the possession of Ramchandra Kalsangra, an absconding accused, she had said.
Some of the witnesses, whose statements were used to implicate her, later retracted and filed complaints of torture by the Maharashtra Anti-Terrorism Squad (ATS), her plea said.
Earlier, the central agency, in its charge sheet filed on May 13, had dropped all the charges against Pragya and five others, citing lack of evidence.
Nisar Ahmed Sayyed Bilal, who was among those injured in the blast, had filed an intervention application and opposed her plea.
Seven people were killed in the blast at Malegaon, a predominantly Muslim town in north Maharashtra, on September 29, 2008.
Pragya was charged by the Maharashtra ATS in 2009 saying it was her motorcycle that was used to plant the bomb.