Police sources said that Malik, who returned from Pakistan after over seven-week stay yesterday, was detained at the airport and escorted to his home at Maisuma.
Malik, however, claimed that he has been put under house arrest.
"Malik was taken into custody by police within the airport premises and later taken out through the back gate," a spokesman of JKLF said.
The sources said the step was taken due to apprehension of breach of peace following Malik's return to the Valley.
The separatists have threatened to continue the protests till their demand for return of mortal remains of Guru and JKLF founder Mohammad Maqbool Bhat who was also hanged in Delhi's Tihar jail on February 11, 1984, is met.
Malik has been under attack for meeting terror outfit Lashker-e-Taiba (LeT) chief Hafeez Saeed in Pakistan and his return to national capital yesterday saw protests by Shiv Sena activists at the airport.