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The United Nations has confirmed at least one case of cholera in flood-ravaged Pakistan, where a second wave of water continues to threaten parts of Sindh province, foreign media reported.

The cholera case was reported in Mingora, the main town in the northwestern Swat valley, which has seen some of the most extensive damage.

Maurizio Giuliano, a spokesman for the United Nations Office for Humanitarian Affairs, said on Saturday the world body had stepped up its efforts to treat cases of diarrhoea, which already affects more than 36,000 people in northwest Pakistan.

"Given that there are concerns about cholera, which is a very deadly disease, what we've started to do instead of testing them for cholera is to treat everyone for cholera," he said.

Unsanitary conditions and a lack of safe drinking water have created the potential for serious disease outbreaks, according to medical workers.

Flooding has killed more than 1,600 people in Pakistan since July 29, and the UN fears the final death toll could be far higher. Millions of acres of crops have been submerged, and more than 14 million people have been affected by the floods.