Special judge Manoj Kumar Sinha sent the trio to judicial custody after they were produced in his court here.
The lawyer representing NIA in the court Lallan Sinha said the three have been booked under 150 Railway Act, sections 3 and 4 of the Explosive Substance Act and other sections under the IPC.
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 playing a role in the derailment of Indore-Patna Express near Kanpur on November 20, 2016 in which around 150 passengers were killed.
The three were allegedly involved in more than a dozen criminal cases and were roped in by Nepalese contacts to trigger train mishaps in India, Rana had said.
Their arrest had come 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.
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