The highly virulent H5N1 strain of the virus was identified at a chicken farm in Dordogne in November, prompting several countries including Japan and China to ban French poultry imports.
In late November, Japan also stopped importing French foie gras, a luxury food prized for festive celebrations but controversial because its production requires force-feeding the birds.
Since then H5N1 has been detected on 69 farms in southwestern France, where the bulk of French foie gras is produced.
The agriculture ministry's order allows farmers to continue raising the birds they have, but they may not take on new chicks until after a cleanup that is to begin on Monday, the agriculture ministry said in a statement.
The process of specially fattening geese and ducks to produce foie gras (fatty liver) takes 12 to 15 weeks.
After the current stock is treated, the farmers must freeze their production while their farms are thoroughly cleaned and disinfected, the statement said.
Production could resume in May or June, but the timeline is still being hammered out, it said.
That will be in time for the poultry farmers to be able to produce foie gras for the next festive season, the statement said.
Japan's foie gras ban, which became effective on November 26, will be lifted 90 days after all affected French poultry farms finish culling their birds and conclude necessary sanitary procedures, according to the Japanese agriculture ministry.
For the first eight months of 2015 Japan was the top global importer of foie gras, according to a French industry group.
France, which produces 75 percent of global foie gras, exported 4,934 tonnes of it in 2014.