The JKLF (Jammu Kashmir Liberation Front) leader was to begin his 48-hour-long hunger strike today but police had denied permission for the protest at Jantar Mantar.
As a preventive measure, Malik was taken into custody last night. "He was flown to Srinagar in a SpiceJet flight," sources said.
Malik was apparently to go ahead with his 48-hour protest from today till Sunday.
The report also said Malik had been involved in "anti- national" activities in the past, they said.
The JKLF leader had shared dais with Lashkar-e-Taiba founder and India's most wanted terror mastermind Hafiz Sayeed when he had staged a protest in Islamabad against the hanging of Guru.