"As per the directives of CAA (Civil Aviation Authority), the air space over Northern areas will remain closed on Wednesday. Inconvenience regretted," Danyal Gilani of the Pakistan International Airlines (PIA) tweeted.
He said all flights to Gilgit, Skardu and Chitral in the Gilgit-Baltistan region were cancelled.
The spokesperson didn't elaborate why the CAA imposed the airspace restrictions.
But the Express Tribune suggested that Pakistan's warplanes may have been engaged in a takeoff and landing rehearsal at Chitral amid "threats from India".
This followed the Sunday attack at a military base in Uri - close to the de facto border that divides Jammu and Kashmir between the two countries.
