Hundreds of homes and thousands of hectares of cultivated land were destroyed in the northwest and Pakistani Kashmir, with the main highway to China reportedly cut off and communities left isolated.
The death toll dwarfed even the 152 killed when a Pakistani passenger jet crashed into hills overlooking Islamabad on Wednesday and capped a week of tragedy in the nuclear-armed nation of 167 million.
Pakistan's northwestern Khyber Pakhtunkhwa province, where impoverished families live in remote mountain villages, was the worst affected.
"We have so far gathered the figure of 325 deaths due to flash floods in the northwest and (Pakistan-controlled) Kashmir," Anwer Kazmi, spokesman for Pakistan's largest charity the Edhi Foundation.
"Our officials have got reports of at least 300 deaths in Khyber Pakhtoonkhwa province while 25 people died in Kashmir's capital Muzaffarabad.
"We have not collected the complete figures from some districts and fear the number of casualties is much higher," he said.
The meteorological department said an "unprecedented" 312 millimetres (12 inches) of rain had fallen in the last 36 hours in the northwest but predicted only scattered showers during coming days.
Government officials put the death toll at 232.
"At least 181 people have died and more than 60 are missing in the province," provincial relief commissioner Shakil Qadir told AFP.
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