Sources said Malik has been taken into custody under sections related to preventive custody.
Malik was apparently to go ahead with his 48-hour protest from tomorrow till Sunday.
The decision to deny permission for his protest came after security agencies submitted a report to the Union Home Ministry that giving permission to Malik to hold protest in Delhi may create law and order problem.
The JKLF leader had shared dais with Lashkar-e-Taiba founder and India's most wanted terror mastermind Hafiz Saeed when he had staged a protest in Islamabad against the hanging of Guru.