"A case has been registered against Andrabi at Nowhatta police station under Section 13 of Unlawful Activities Prevention Act," a police officer said.
He said investigations have started into the alleged hoisting of Pakistani flag by the separatist leader on Monday.
"Further action in the case will be taken as per rules," the officer said when asked if the firebrand separatist leader will be arrested.
A controversy erupted following media reports claiming that Andrabi had hoisted flag of Pakistan and sung its national anthem on March 23.