Chief Metropolitan Magistrate (CMM) Manoj Kumar sent Shah to 14 days judicial custody in Tihar jail after he was produced in the court before the expiry of his 15-day police remand.
Delhi Police's Special Cell has been quizzing Shah since March 21, after it was given his custody. Police Saturday moved an application saying that the accused be sent to jail as they do not need to quiz him anymore in their custody.
Shah, a resident of Dardpora village in Kashmir's Kupwara district, was arrested from Uttar Pradesh's Gorakhpur March 20 when he entered India through Sunauli border check post of Kathmandu where he had flown in from Karachi.
There are two conflicting versions on Shah's arrest. While Delhi Police claim he was part of a terrorist plot attempting to launch a fidayeen (suicide) attack in the capital, Jammu and Kashmir Police say he was on his way back home from Pakistan to surrender under the rehabilitation policy of the government.
The home ministry Monday asked the National Investigation Agency (NIA) to probe the case.
The Delhi Police has booked Shah for waging war against the country claiming he was planning to carry out terror attacks in the national capital to avenge the hanging of Parliament attack convict Afzal Guru.
Police in their application said that Shah, during interrogation, has revealed that he is a trained militant of banned terror group Hizbul Mujahideen and was settled in Muzaffarabad in Pakistan-administered Kashmir.
It further told the court that in January 2013, Shah and his associate Manzoor, a resident of Jammu and Kashmir, were directed by top leader of the outfit to carry out terrorist attacks in Delhi. Shah's associates, including Manzoor are missing, said police.
Police further added that upon disclosure of the accused, a huge consignment of arms, hand-grenades, explosive material and other incriminating material was recovered from a guest house in Jama Masjid area here.
"It was also informed that two-three terrorists have travelled from Jammu and Kashmir to set up a base in some hotel in Jama Masjid area, Delhi and the terrorists who have to execute the strikes may enter India through the India-Nepal border at Gorakhpur, UP or Tanakpur in Uttrakhand," said police in their application before the court.