Six to seven inches (160-180mm) of rain fell in just five hours overnight.
Rivers have risen by more than 20ft (6m) with people “stranded on rooftops” whilst they wait for emergency services.
The prefect of Aude, Alain Thirion, said: “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.”
Six helicopters were deployed to the town but the horrendous conditions have made the rescue mission more difficult.
Around 250 firemen and 100 police officers were involved in the effort.
The flash floods struck without warning, the force of the storm brought down trees, power pylons, and swept away cars.
The villages of Conques-sur-Orbiel and Villardonnel were among the worst affected areas, with waters rising as high as the first-floor windows of some houses.
Forecasters warn the rain will continue throughout the morning and water levels are expected to rise further.
Schools in the area were closed and residents were told to stay at home.
Torrential rain storms are not uncommon in France at this time of year.
Meteorologists have said exceptionally warm sea water along the Mediterranean coast may be intensifying the rains.
The year so far is France’s hottest since 1900, according to the state meteorological service.