Judge Manoj Kumar Sinha accepted NIA's prayer for custody of the three.
The same court had yesterday sent them to judicial custody till February 17.
Motilal Paswan, Mukesh Yadav and Umashanker Patel were arrested from Bihar's East Champaran district on January 17.
During the course of investigation, Paswan admitted to playing a role in the derailment of Indore-Patna Express near Kanpur on November 20, 2016 in which around 150 passengers were killed.
After their arrest, East Champaran Superintendent of Police Jitendra Rana had claimed that the trio had confessed to have worked for a Nepali contact suspected to be connected with ISI.
They were arrested in the course of a probe into the murder of two persons in Nepal in December last year for failing to explode bombs on railway tracks at Ghorasahan area of East Champaran district on October 1, 2016, the SP said.
NIA took over investigation in the wake of disclosures during the probe.
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