Chief judicial magistrate of Bankshall court Md Mumtaz Khan also sent five others arrested in the case to judicial remand.
Khalid, one of the prime accused in the Burdwan blast, Sk Rahmatulla and Amjad Sheikh will be in NIA remand till November 28.
The court granted judicial custody of Rajiya, Hashem Mollah, Jia Ul Haq, Alima and Abdul Hakim as prayed for by NIA till December five.
NIA counsel Shyamal Ghosh prayed for the custody of Khalid, who was arrested at Hyderabad on November 17, saying he was directly involved in the case.
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It was also submitted that he ran terror camps in the bordering areas of Bangladesh and Myanmar as also in West Bengal.
The counsel prayed for extension of police custody of Sk Rahmatulla and Amjad Sheikh for eight days claiming that they needed to be questioned further in connection with chemicals bought by Amjad, who worked for a pharmaceutical company here and procured vital components for making IEDs at Burdwan by Bangladeshi terrorists at a house in Khagragarh.
An accidental blast there on October 2 which killed two persons brought to the fore the activities of jihadi elements from Bangladesh.