However, it allowed Dwivedi to visit his house in Kanpur under a police escort for which he will have to pay.
"The court rejected his bail application. However, it allowed him to go to his native place along with the police escort from January 19 to February 1", special NIA prosecutor Avinash Rasal said.
Dwivedi had earlier, though his lawyer Kanishk Jayant, moved an application seeking temporary bail.
The court has also set out 12 conditions which Dwivedi will have to adhere to for going to his native place.
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The court also directed that Dwivedi will not leave the jurisdiction of Kanpur city.
"Accused shall not contact any witnesses concerned with the case and he will not speak to any person over phone without the prior permission of the escort party", it said.
12 persons, including Sadhvi Pragya Singh Thakur and Lt.Col Prasad Purohit, were arrested for carrying out a blast at Malegaon on September 29, 2008, killing six persons and injuring 100 others.
Following a Supreme Court order, a special court under the provisions of NIA Act has been constituted to exclusively hear the case.