Rescue helicopters were waiting for clearer weather before they could launch rescue 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, Reuters reported.
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.
The flash floods struck without warning. At least one victim was swept away by raging waters while sleeping, Thirion said.
Water levels were expected to continue to rise in the area on Monday, with rain forecast until late in the morning. Schools in the Aude area were closed and residents were told to stay at home.
Torrential rains are not uncommon in France at this time of year, but meteorologists have said that exceptionally warm sea water along the Mediterranean coast of southern France may be intensifying the rains.
The year so far is France's hottest since 1900, according to the state meteorological service.