The agency will question Bhavesh Patel about the conspiracy behind the bombing as well as the murder of RSS member Sunil Joshi, official sources said.
NIA sleuths arrested Patel from here yesterday and produced him before a designated NIA court in Jaipur today which sent him to 15 days custody, they said.
Patel is alleged to be one of the main persons involved in planting the explosives at the dargah in October 2007 that left three persons dead and 20 injured.
The NIA has arrested at least nine persons in connection with the murder of Joshi and explosions in Samjhauta train, Malegaon and Mecca Masjid blasts in Hyderabad.
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Patel is alleged to have planted the bomb inside the shrine on the direction of Joshi, the sources said, adding the accused was involved in planning the terror act as well.
The arrest of the accused is expected to unravel the fate of other members of the terror module who have been absconding over a period of time.