As soon as Friday prayers got over at Jami Masjid in the Nowhatta area of the city, a group of youths waved the controversial flags and raised pro-separatist and pro- Pakistani slogans, officials said.
They said police had to fire tear gas shells to disperse the stone-pelting mob and restore law and order.
The officials said that the youths also set fire to the tricolour before marching towards Nowhatta Chowk on their way towards Khanyar Chowk.
There is no report of anybody being hurt in the incident, they added.