Protestors led by chairman of All Parties Migrants Coordination Committee (APMCC) Vinod Pandit said he was "in a habit of making anti-national statements".
They demanded sedition charge be slapped against Abdullah for his recent statement in which he had "sided with the separatists".
"We demand Farooq Abdullah should be booked for sedition for his statement in favour of Kashmiri separatists," APMCC national spokesman King Bharti said.
Addressing his party workers at a function to mark the 111th birth anniversary of his father and party founder Sheikh Abdullah at Hazratbal, Farooq had asked Hurriyat leaders not to go separate ways saying "be united and we are also standing with you".
"Do not think of us as your enemies, we are not. But we are not ready to tread the wrong path. So, I am telling you from this sacred place that you (Hurriyat) move forward, we are with you till your steps are on the right track and till you take this nation forward in a right manner," he had said.
Meanwhile, state BJP accused National Conference of supporting those behind the unrest in he Valley that started after the killing of Hizbul Mujahideen terrorist Burhan Wani.
"The statement of Farooq Abdullah proves beyond any doubt that NC and its workers are behind the ongoing agitation launched by separatists and Pakistan-sponsored terrorists in the Valley," BJP state spokesman Virender Gupta said.
"He needs to come clean and tell whether he endorses stone pelting by youth, burning of schools, calls of bandh by Hurriyat which is being observed for the last more thanfive months," he said.