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Farmers blamed a government program for reintroducing brown bears from Slovenia after most of the native bear population was wiped out by hunters.
"Pastoralism, which is a guarantor of biodiversity and of a living and welcoming mountain region, is not compatible with the reintroduction of large predators," the French Farmer's Federation said in a statement quoted by The Local.
There are believed to be 30-35 brown bears currently living in the Pyrenees mountains, which straddle the border between France and Spain.
The French government is expected to compensate the farmer who owned the sheep flock for his loss.