The female bear, who was travelling with her cubs, bit him as he was hunting in the Seix region of Ariege, a source close to the case said.
Rescued by the local gendarmerie, he was transported to the intensive care unit of a hospital in Toulouse with a wound to his leg at the level of his femoral artery, officials at the prefecture in Ariege said.
One source close to the case said he was in a serious condition.
The hunter told local officials he had been out with a group of other hunters on the trail of a boar, when the female bear, who was travelling with her cubs, attacked him.
After being wounded, the hunter shot the bear twice, killing it.
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The local gendarme unit was called out to rescue him at around 3:30 pm (1430 GMT). They discovered the body of the bear a few metres from where they had found the hunter.
An investigation has been opened into the incident, the prefecture in Ariege said.
One local official told AFP on Saturday: “This is really what we feared.”
“Today, you can really see that cohabitation is complicated,” said Christine Tequi, president of the Ariege department council.
The brown bear had nearly disappeared in this part of the world when France began a programme of reintroducing them, importing them from Slovenia.
Today, there are around sixty of them in the Pyrenees range, leading to increasing tensions with local farmers, because of the threat they pose to their livestock.
In 2020, three bears were illegally killed in the Pyrenees: two of them in Spain and one in France. The French government has committed to replacing any bear killed by a man.