The Home Ministry has also sought reports from the Bihar government and central security agencies regarding the arrest of Moti Paswan, Uma Shankar and Mukesh Yadav and their disclosures to Bihar Police.
Official sources said the role of ISI will be probed by the NIA and find out whether there was a larger conspiracy involving ISI agents based in Nepal and Dubai.
If the claim of the three accused turns out to be true, it would be the first such case of train derailment in India carried out at the behest of the Pakistani agency, the sources said.
A report is also being sought from RAW about ISI activities in Nepal and India.
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The three persons arrested yesterday in East Champaran district in Bihar had told police that they were paid Rs 3 lakh to plant explosives at Ghorasahan in the district on October 1, 2016.
A report is said to have come from Nepal confirming the Bihar Police's claim that Pakistan's ISI had paid Rs 30 lakh to its agent Brajesh Giri for triggering blasts on rail tracks targeting popular trains in Bihar, the sources said.
The role of ISI in the recent train disaster in Kanpur was being suspected after Bihar Police had yesterday arrested three persons who they claimed were working for the Pakistani spy agency to target Indian railways.
The ISI link to the November 20 train disaster, in which 150 people were killed, was being suspected after the interrogation of the trio, police had said.
During interrogation, the three arrested persons provided some "positive lead" about the Indore-Patna Express derailment in Kanpur, District Superintendent of Police Jitendra Rana had said.