Hundreds of worshippers had to flee morning Mass at Saint Donatien in the city of Nantes as the flames took hold.
Revd Benoit Bertrand told local media that the blaze started during the service at around 10.30 local time.
"I see flames still escaping," he said on BFM television.
French authorities have confirmed that 40 firefighters are tackling the blaze which has spread to the roof of the church.
Smoke from the blaze can be seen across the western city.