Assemanand's bail plea, filed on the ground that the NIA failed to file a charge sheet within 90 days, was rejected by the Court of District and Sessions Judge.
Aseemanand denied having made any statement to the National Investigation Agency about his involvement in the Samjhauta case.
Assemanand, through his counsel Subhash Gehla, charged the NIA of pressurising and torturing him mentally and physically to extort a statement from him.
A total of 68 people, mostly Pakistanis were killed in Samjhauta Express blast, at Panipat''s Diwana village, about 80 km from Delhi.
Earlier on May 7, a CBI court at Jaipur, Rajasthan had also rejected his bail application in the 2007 Ajmer Dargah blast case, extending his custody till the next date of hearing on May 14.
Apart from Ajmer Dargah blast, which claimed three lives and left 15 others injured, Aseemanand is an accused in several other blast cases across the county including those at Hyderabad's Mecca Masjid and Malegaon.
He was arrested by the CBI last year from Haridwar in Uttarakhand for his alleged role in the Mecca Masjid blast case.