Farmers in southwestern France blocked roads and set fire to bales of hay on Saturday to protest the culling of cows due to a skin disease, as the government said one million cattle would be vaccinated.

French farmers have been angry over what they see as the government's heavy-handed response to an outbreak of nodular dermatitis, widely known as lumpy skin disease.

On Friday, veterinarians slaughtered a herd of more than 200 cows in the village of Les Bordes-sur-Arize near the Spanish border after discovering a single case of the sickness.

Police had to disperse angry farmers as they escorted in a team to carry out the culling.

Several unions have said that slaughtering whole herds is ineffective, calling for blockades across France "to put an end to this madness."

On Saturday, dozens of tractors blocked traffic, while others parked in front of public buildings, as farmers set fire to bales of straw and tyres.

Nearly 150 kilometres of the A64 motorway between Bayonne and Tarbes were closed to traffic due to blockades that began late on Friday.

Lumpy skin disease, which cannot be passed to humans but can be fatal for cattle, first appeared in France in June.

The official strategy to stamp out what the authorities describe as a very contagious disease has been to slaughter all animals in affected herds, and carry out "emergency vaccination" of all cattle within a 50-kilometre radius.

"It's the extermination of cows and farmers," said Leon Thierry of hard-line farmers' union Coordination Rurale (CR), who protested in the town of Briscous with more than a dozen farmers and around 40 tractors.

"It is out of the question that in the Pyrenees we should slaughter animals that are not sick, that are healthy, because they belong to a herd from which, supposedly, a sick animal has emerged," he said.

Around a hundred farmers gathered in Carbonne located some 40 kilometres southwest of Toulouse, setting up camp on the A64 highway.

"They deploy riot police to kill 200 cows, but you don't see them at the drug-dealing spots!" said Benjamin Kalanquin, 24, who works not far from the farm where the entire herd was slaughtered. (AFP)