"The H5N1 virus is confirmed as the cause of the death of turkey farmed in the Ain department (of eastern France)," the ministry said in a statement.
Officials became alarmed on Thursday when more than 400 birds were found dead of illness on the turkey farm near Joyeux.
It’s the third confirmed case of H5N1 bird flu in France and the first time the highly pathogenic strain has been found on a farm in the EU. All other cases of the disease found in the 26-nation-union were discovered in wild birds.
In total, eight EU countries have so far confirmed cases of the deadly strain: Austria, France, Germany, Greece, Hungary, Italy, Slovakia and Slovenia.
In other developments, H5N1 was found for the first time in the former Soviet republic of Georgia after dead swans tested positive to the strain. The virus has also spread from northern Germany to the south of the country.
Containing bird flu
The confirmation of the H5N1 virus in a commercial poultry farm has raised concerns over the how it will affect consumer confidence and how it will impact efforts to contain the virus.
There are questions as to how animals kept in a confined space could have contracted bird flu.
The Poultry Industry Federation (FIA) said that the infected turkeys may have been contaminated by dried duck droppings on the straw used as their bedding.
French Prime Minister Dominique de Villepin said it would take appropriate steps after further investigation into the cause of infection.
Previously French authorities had confirmed two cases of H5N1 bird flu, both in wild ducks also found in the Ain region.
On Friday, five more suspected cases were reported in wild swans in the same area, sparking the surveillance of a third of the Ain department.
French poultry sales have already fallen 25-30 per cent on the same period last year causing many poultry firms to reduce staff numbers.
Greatest fear
Scientists and governments are fearful that the virus could mutate into a form that is easily transmissible between humans, rather than just from bird to human infection.
The greatest worry is that such a mutation could spark a pandemic that could kill millions.
Since the outbreak of H5N1 bird flu in 2003, 92 people have died, mostly in Asia where the disease was first identified.