The Chitral valley in Khyber Pakhtunkhwa province was the worst-affected as the floods snapped most road links to and from Chitral city, Geo News reported.
A rescue operation has been initiated to aid the affected population and an emergency imposed in Chitral as rains continued.
Several parts of Punjab province were also affected. At least 100 villages and settlements were inundated around its capital Lahore, which faced a medium-level flood.
Officials said water levels in the river Indus were rising.
Abdul Aziz Soomro, the in-charge of the control room at Sindh province’s Sukkur Barrage, said water levels were expected to rise further in the next 24 hours at Guddu and Sukkur barrages.