The JMB operative was identified as Habibur Rehman Sheikh alias Habibur Kabore Shaik or Habibur S.K., was arrested by the NIA from the Dodabalpur area of the Karnataka capital.
According to senior officials of the counter-terror probe agency, Sheikh was a close associate of senior JMB leader Jahidul Islam alias Kausar and was associated with other JMB leaders like Rahamatullah Sheikh and Moulana Yusuf.
"He was named in the charge-sheet filed by the NIA in the case in March, 2015 for his direct involvement in the conspiracy of the JMB to wage war against governments of India and Bangladesh," an NIA official said in Delhi.
The official said that Sheikh was an active member of JMB's Bolpur Module in West Bengal and had attended a number of training camps conducted by the JMB.
The JMB operative was produced before the NIA Special Judge in Bengaluru earlier in the day, which has granted five days' transit remand for producing him before the Special NIA Court in Kolkata.
At least two persons died and another was injured in a bomb explosion at a house in the Khagragarh locality of Burdwan on October 2, 2014. The Bangladesh government banned the JMB in 2005, while India banned it in May this year.
( With inputs from IANS )