EasyJet cancelled more than 100 flights while Ryanair cancelled 26 flights, including six to and from Edinburgh Airport, and passengers waiting on flights which were leaving faced delays of up to six hours.
A further four Ryanair Edinburgh Airport services to Alicante and Malaga are expected to be cancelled on Wednesday.
The airline said it had cancelled 15 per cent of its planned flights after a request from French authorities to ease the pressure on air traffic control services.
Kenny Jacobs, Ryanair's Chief Marketing Officer, apologised to customers and called on the EU Commission to remove the right to strike from Europe's air traffic controllers,
He said French air traffic controllers have" deliberately initiated industrial action at the busiest time of the year in order to cause maximum chaos".
He said: "Ordinary people who work hard all year to take a well-earned holiday have had their travel plans disrupted through no fault of theirs, or of Ryanair's, because of the selfish actions of so few."
The UNSA-ICNA union, the third-largest air traffic controller union in France which called the strike, says government funds earmarked to modernise the sector over the next four years are insufficient. The industrial action is due to last until the end of Sunday.
EasyJet said that 65 per cent of their flights travel over French airspace and "as such we have seen significant delays to many of our flights".
In a statement the airline said: "We are disappointed at this unnecessary strike action which has the potential to cause considerable disruption and cancellations for passengers and airlines across Europe.
"Despite the fact that this disruption is beyond easyJet's control we will do everything possible to minimise the inconvenience to our customers. We will proactively provide advice for our passengers through our website, text messages and flight tracker tool."