Reverend Benoit Bertrand said the blaze broke out on Monday after morning Mass, with worshipers evacuated from the building.
Rev Betrand said: “I see flames still escaping”.
The fire spread quickly, ravaging the rooftop of the historic building, as fire-fighters in their numbers were deployed to the scene to try and extinguish the flames.
The blaze reportedly broke out at 10:30 local time (08:30 GMT), but the cause has not yet been established.
The Basilica of Saint Donatien was consecrated in 1889.
The other main church in Nantes, the Cathedral of Saint Pierre and Saint Paul, suffered a similar roof fire in 1972 just 28 years after it was damaged during World War Two.