Ayrault flew over the Var on Monday morning, landing at La Londe-les-Maures, a town where a 70-year-old man died when trapped by the waters in his cellar.
The prime minister promised a "huge effort" to "reconstruct" the flood-ravaged areas.
"We'll come to the rescue, that's what we're here for," he said.
A man who was reported missing was found on his boat overnight, La Londe-les-Maures's mayor, François Canson, reported.
About 600 residents were affacted by flooding at la Londe with many more affected in nearby Hyères, where farming land was badly hit and streets were swamped with mud.
Another man died when his car was swept away on a flooded road.
Emergency helicopters were deployed overnight, with 500 firefighters and 200 police mobilised.
By lae Sunday at least 150 people had been airlifted from the worst-hit areas and others were being moved out by boat.
The rain let up in the Var on Monday, although authorities maintained a flood warning for three rivers there and announced a new warning that the River Rhone might flood in the Gard and Bouches-du-Rhone.