The work stoppage comes at the height of the tourist season in a nation that attracts more foreign visitors than any other country in the world, and follows a rail protest that affected services abroad and domestically and is still continuing in some areas.
The country's civil aviation watchdog said around one in five flights going to and from several big cities in southern France, or taking off from Paris to the south, Spain, Portugal, Morocco, Tunisia and Algeria, were cancelled and passengers were experiencing delays on other services.
EasyJet meanwhile cancelled 28 flights and British Airways said eight flights had been affected.
Not all air traffic controllers are striking, but those stopping work are protesting against what they say is a lack of sufficient funding allocated for their sector, which they say is in dire need of modernisation.
They want airport fees for airlines to increase by 10 percent, companies want them to go down, and the government is caught in between.
The system used in the country to enhance radar monitoring and for separation of air traffic dates back to the 1980s, and is due to be replaced by a new system.
The tools used to control air traffic are also in need of change.
According to the SNCTA, for instance, all radar screens in the Aix-en-Provence control centre in southern France were recently "urgently" changed after around 20 screens suddenly went blank over the space of 18 months.
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