"I have asked NIA to probe the case," Union Home Minister Sushilkumar Shinde said here.
J and K Chief Minister Omar Abdullah had spoken to Shinde on Saturday and demanded a "speedy and time-bound" probe by NIA into the circumstances leading to the arrest of Liyaqat.
While the Delhi Police claimed that he was a Hizbul Mujahideen terrorist, its Jand K counterpart insisted that he was one of those who had exfiltrated in 1990s and had returned to India to surrender under the rehabilitation policy of the state government.
The list of 90 people was prepared in 2012 and included the name of Liyaqat after having been vetted by the J and K police and central security agencies.
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Delhi Police contended that it had information about arrival of Liyaqat and the input was based on the intelligence generated by the force itself.
The police has also prepared a sketch of an accomplice of Liyaqat who had allegedly dumped the weapons at a guest house in Old Delhi.
They claimed he was a Hizbul Mujahideen terrorist who planned attacks to avenge the hanging of Parliament attack convict Afzal Guru.
The J and K police, however, supported the claims of Liyaqat's family that he was a former militant who had surrendered before SSB at the Sanauli check-post on the Nepal border and was in a group returning from PoK under the rehabilitation policy. He was arrested on March 20 from Indo-Nepal border.