The Interior Ministry said three “everyday heroes” had died while helping people caught in the bad weather affecting the country’s south.
Contact was lost with the helicopter during a reconnaissance and rescue mission on Sunday night, the ministry said.
Jean Garat, a pilot, Michel Escalin, a mechanic, and Norbert Savornin, from a local fire brigade, were found dead near Marseille in the early hours of Monday.
The administration for the Var region said two other people were killed in the storm, including a stable owner whose vehicle was swept away by floodwater as he tried to check on his horses.
Six people were killed in flooding around France’s Mediterranean coast a week ago.
The Interior Ministry said an investigation into the civil defence helicopter's crash is underway.
“Our country loses three everyday heroes who gave their lives to protect French people,” a ministry statement said.
Emmanuel Macron, addressed their colleagues in the fire brigade and rescue service, as well as their families, to say they had “the support of the nation that they have served so much”.
Heavy rain has also brought flash floods and landslides to parts of Greece and Italy in recent weeks.
Additional reporting by Associated Press