The warrant was issued yesterday by the designated Maharashtra Control of Organised Crime Act Court (MCOCA) on an application moved by Maharashtra ATS seeking his production in the arms haul case.
Taking the warrant, the ATS will now go to a Delhi local court to seek Jundal's custody, they added.
In the arms case, a Maharashtra ATS team had chased a Tata Sumo and an Indica car on the Chandwad-Manmad Highway on May 8, 2006, and arrested three terror suspects while seizing a huge cache of 30 kg RDX, 10 AK-47s and 3,200 bullets from the vehicle and along the road.
The Indica, which was allegedly driven by Jundal, who hails from Beed district, however, could not be intercepted at that time, according to ATS.
Jundal had allegedly driven the car to Malegaon and handed it over to an acquaintance before disappearing, ATS said.
Investigators later seized 13 kg of RDX and six AK-47s from Malegaon and 50 grenades from Ankai village near Manmad in Nashik district.
A month later, police claimed that Jundal had fled to Bangladesh and later crossed over to Pakistan.
A total of 21 terror suspects were behind bars in the case.
Jundal was arrested in Delhi on Monday for his alleged complicity in the 26/11 terror attack.
Two days back, another Mumbai court had issued a production warrant against Jundal in the 26/11 case.