Karim, on whom a cash reward of Rs five lakh had been announced by the NIA, was arrested from Jharkhand where he was hiding since the blast took place in Burdwan on October 2.
According to the NIA statement, he was an active member of JMB and was "engaged in manufacturing and transport of bombs to different locations.
"Since the time of incident he has been absconding to evade arrest," it said. After the probe into the blast, NIA and West Bengal police had recovered 39 similar bombs from his house located at Badshahi Road in Burdwan.
After the first blast on October 2 in Burdwan, injured accused Abdul Hakim had called up Karim for providing assistance and evacuation.
NIA is hopeful that his interrogation may throw fresh leads and evidence in the investigation of this case.
So far 12 people have been arrested in this connection.