French weather agency Météo-France said as much as 700 millimetres of rain fell in in 48 hours in some local areas in the southern regions of Ardèche and Lozère.
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Clean-up operations are under way after two days of torrential rain caused the worst flooding central France has seen in 40 years.
France's prime minister Michel Barnier said that firefighters and other rescue teams have been involved in about 2,300 operations, some of them lifesaving, in several parts of the country.
"We must prepare, with climate change, to face risks and disasters in all areas more better and more frequently. The more we prepare together at the level of the countries that are part of this European entity, the better it will be. I have long believed that prevention costs less than repair," he said.
"I believe we must go further and that these crises across all categories - such as maritime disasters, industrial disasters, tsunamis, earthquakes, major floods, and large pandemics, as we have seen, along with the terrorist risk - should all be anticipated and prepared for together at the European level."
Barnier also praised an alert system, FR Alerte, which was used for the first time and sent text messages urging people in the concerned areas to delay or cancel their planned trips and stay in a safe place.
Over 1,000 people were evacuated from several areas but most of them were able to go back home on Friday.
French weather agency Météo-France said as much as 700 millimetres of rain fell in 48 hours in some local areas in the southern regions of Ardèche and Lozère.
National railway operator SNCF halted regional trains between the cities of Lyon and Saint-Étienne on Thursday saying the tracks were impassable.
Local train services will remain disrupted for several days, it said.
And a main highway between the two cities also was inundated and remained closed on Friday.
Météo-France lifted its red alert for bad weather on Friday morning but still warned of potential heavy rain and floods in southwestern areas.