At least 13 people including a nun have died and five have been seriously injured in flash foods in southwestern France in an area popular with tourists and expatriates.

The Aude department, home to the medieval fort city of Carcassonne, sustained seven months of its average rainfall in one night in the worst floods in the area since 1891.

A nun was swept to her death by rising waters in the village of Villardonnel, where her convent was partially destroyed, and at least four died overnight in Villegailhenc, local authorities said.

A sixth person also died in Trèbes and local authorities raised the death toll to 13.

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"This is a temporary toll and as reconnaissance continues during rescue efforts, it is possible it could get worse," warned Edouard Philippe, the Prime Minister.

The threat of further flooding has not yet abated, according to Vigicrues, the French agency responsible for monitoring water levels. A thousand people were evacuated from the town of Pezens due to fears of a dam bursting.

Six helicopters were dispatched to help rescue people from roofs, but continuing poor weather was hampering operations, the prefect of Aude, Alain Thirion, told BFM TV.

"We have people stranded on rooftops. We're going to have to use aircraft to evacuate them because we cannot reach them by boat given the force of the water. It's too dangerous," he said.

Among the worst hit areas were the villages of Conques-sur-Orbiel and Villardonnel, where waters rose as high as the first-floor windows of some houses.

One person was also injured when a house collapsed in Cuxac, while in the space of five hours "between 160 and 180mm of water fell on Carcassonne", said Thirion.

Rescue workers retrieve a body from floodwaters in the town of Trebes, southern France. Photo / AP
Rescue workers retrieve a body from floodwaters in the town of Trebes, southern France. Photo / AP

The water level of the river at Trèbes reached 7m, the highest in 127 years, while in Conques, there was up to 2m of water in the streets.

Firemen responded to more than 250 calls while in villages north of Carcassonne, all roads were cut, schools closed, and people were asked to stay at home.

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Around 15 towns were in a "difficult situation" while six were in a "worrying state".

In Saint-Etienne d'Albagnan, in the neighbouring Hérault, a helicopter rescue operation was underway to help people who had sought refuged in trees to escape floodwaters.

A French Gendarmerie helicopter winches a rescue worker over the town of Trebes, southern France. Photo / AP
A French Gendarmerie helicopter winches a rescue worker over the town of Trebes, southern France. Photo / AP

Some 600 firemen were helping in the effort, including seven aquatic rescue teams.

Six other departments were also hit by the storms from the eastern Pyrenees to Aveyron further north.

Torrential rain at this time of year is not uncommon in France but meteorologists have warned that exceptionally warm sea water along the Mediterranean coast may be fuelling this year's floods.

This has been France's hottest since 1900, according to the state meteorological service.

The deaths came just days after intense rain sparked flash floods in the Spanish holiday island of Majorca, killing 12 people, including two Britons. Yesterday, near-hurricane winds hit Portugal, leaving hundreds of thousands of people without power before carrying heavy rain on into Spain.

Twenty-seven people suffered minor injuries.