Recent bird flu outbreaks in eight European countries including neighbouring Switzerland and Germany have put French authorities on alert.
A full 64 departments in France have had their risk level raised from "negligible" to "elevated" after the H5N8 strain of the virus was discovered abroad.
"Since recent cases in our European neighbours mainly affect migratory birds, the ministry has raised the level of risk in wetlands that concentrate wildlife and can be stops on the route of migrating birds," the farm ministry said.
Farmers in these areas have been told to keep their flocks inside or put up nets to ensure no migratory birds come into contact with their own birds.
The warnings include hunting restrictions, which come into play as France's hunting season is in full swing.
The risks of bird flu have kept French authorities on their toes this year, with the ministry launching a three-month ban in May on the production of foie gras following a bird flu scare in the south west of France.
The ban meant that 18 departments weren't allowed to have ducks or geese in their slaughterhouses or production rooms over the period.
In January, poultry farmers in southwestern France were ordered to freeze production of geese and ducks for several months after the highly virulent H5N1 strain was found at a chicken farm in Dordogne.
The new outbreak across Europe, however, is not believed to be connected to the risks earlier this year.