Officials reported that 307 of the deaths were in Khyber Pakhtunkhwa province, where mountainous terrain has been hit hardest by the flooding.
Nine people were killed in Pakistan-administered Kashmir and five in Gilgit-Baltistan, the authority said.
Most victims died in collapsing houses and sudden surges of water, while 21 others were injured.
Rescue teams are continuing to search for survivors in Buner district of Khyber Pakhtunkhwa, where cloudbursts and heavy rains washed away dozens of homes, said Mohammad Suhail, a spokesman for the emergency services.
The meteorological department issued a new warning for further heavy rainfall in the northwest, urging people to take precautionary measures.
Authorities also reported that at least 633 people have died this week in northern Pakistan as a result of floods, with 351 deaths confirmed in Khyber Pakhtunkhwa and Gilgit-Baltistan alone.
The impact has been mirrored across the border in Indian-controlled Kashmir, where flooding has left dozens dead and forced hundreds to evacuate their homes.
Experts say that sudden cloudbursts and intense downpours are becoming increasingly common in the Himalayan regions of Pakistan and India, with climate change contributing to the growing frequency and severity of such disasters.