The Chief Minister took up the matter with Shinde over phone as the latter was away in Maharashtra with President Pranab Mukherjee.
"I have spoken to him and asked for a speedy and time bound probe by the NIA to establish the facts in this case," Omar told PTI here.
A controversy broke over the arrest of Liyaqat Shah by Delhi Police which claimed that he was a Hizbul Mujahideen terrorist who had come to the national capital to plan a suicide attack.
Even the family of Liyaqat at Lalpura, Kupwara in North Kashmir said that they had informed the authorities about his return, which was agreed upon.
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Kashmiri youth who had crossed over to Pakistan-occupied -Kashmir (PoK) in 1990s have been returning to the Valley via Nepal.
The family members of Liyaqat claimed that he entered into India through Gorakhpur in Uttar Pradesh and he presented himself to border guarding force -- SSB. However, instead of handing him to state Police, Liyaqat was given to Delhi Police.