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Fire crews were alerted just before 08:00 am (0600 GMT) to the blaze at the Cathedral of St Peter and St Paul, construction on which started in the 15th century, the emergency operations centre said.
It said the "major fire" was still advancing and 60 firefighters had been dispatched to the scence.
The gothic structure was last hit by fire in 1972. Its roof took more than 13 years to repair.
Another religious building in Nantes -- the Basilica of St Donatian and St Rogatian -- was struck by a fire in 2015 that destroyed three-quarters of its roof.
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In April last year, a fire engulfed Paris's 13th century Notre-Dame Cathedral, causing its steeple to collapse and sending billowing fumes containing toxic molten lead into the air. The structure will take years to repair.
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