The cases were reported and confirmed between the start of the disaster and the end of September, and were spread across the large flooded area, the WHO said in a statement.
"Diarrhoeal diseases including cholera are among the most reported health conditions in many locations affected by the recent floods disaster in the country," the WHO said.
The WHO and other health bodies have established more than 60 centres across the country to deal with diarrhoeal diseases.
In addition to cholera, Pakistan's health ministry reported 26 cases, including three deaths, of Crimean-Congo haemorrhagic fever (CCHF); and over 1,500 laboratory-confirmed cases of dengue fever, including 15 deaths, the WHO said.
"The transmission of both CCHF and dengue fever has intensified in the country with increased incidence and geographic expansion," the WHO said.
"The recent Pakistan floods may have contributed to this upsurge as a result of changes in risk factors for these diseases."
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