Additional sessions judge Gopal Chandra Karmakar directed that the accused Hafez Molla alias Hasan, Rajira alias Razia Bibi and Alima Bibi would be in NIA custody till October 22.
The NIA counsels prayed for 14 days' custody of the accused citing the gravity of the incident, its international ramifications and investigation into the conspiracy angle.
The judge, however, granted 10 days' custody, stating that it would decide on further NIA custody after considering the developments on October 22.
Hafez Molla was brought in after them and was given a seat inside the witness box surrounded by policemen.
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All of them were taken away from the courtroom immediately after the judge passed the remand order.
A fourth accused, Sk Hakim, who was injured in the blast is undergoing treatment at the state-run SSKM Hospital here.
The judge directed that the local police would ensure proper security for Hakim, who is also under arrest.
The Centre had on October 9 decided to hand over the probe to the NIA in which the role of terror groups is suspected.
The NIA has registered cases in the Burdwan blast case under sections 16, 18, 18A, 19 and 20 of the Unlawful Activities (Prevention) Act.
It has also registered cases under sections 286 (dealing with explosive substance), 307 (attempt to murder), 326 (voluntarily causing grievous hurt by dangerous weapons), 120B (criminal conspiracy), 121 (waging war against Government of India), 121A (conspiracy to commit certain offences against the state), 122 (collecting arms with intention to wage war against the state), 123 (concealing with intent to facilitate a design to wage war against the state) and 34 (common intention) of IPC and sections 3 and 4 of Explosives Act.