The carriers believe France is breaking the law by not allowing flights over the country
Aer Lingus and Ryanair are among a group of airlines which have submitted complaints to the European Commission against France over its air traffic controllers' strikes.
The complaint alleges the strikes restrict the fundamental principle of freedom of movement within the EU.
The International Airlines Group (IAG) - owner of Aer Lingus - Ryanair, easyJet and Wizz Air have submitted the complaints.
The airlines are not questioning the right to strike, but say they believe France is "breaking EU law" by not enabling flights over the country during strikes.
It says: "Passengers on overflights are being denied their fundamental freedom to travel between member states not affected by strike action."
Willie Walsh, IAG's chief executive, says: "The right to strike needs to be balanced against freedom of movement.
"It's not only customers flying in and out of France who are affected during French ATC strikes.
"Passengers on routes that overfly France, especially the large airspace that covers Marseille and the Mediterranean, are also subject to delays and massive disruptions. This affects all airlines but has a significant negative impact on Spain's tourism and economy."
Michael O'Leary, Ryanair's chief executive, adds: "Europe's ATC providers are reaching the point of meltdown with hundreds of flights being cancelled and delayed daily either because of ATC strikes or because Europe's ATC don't have enough staff.
"When Greece and Italy have ATC strikes, overflights continue as normal.
"Why won't France do the same? ATC providers (especially in Germany and the UK) are hiding behind adverse weather and euphemisms such as 'capacity restrictions' when the truth is they are not rostering enough air traffic controllers to cater for the number of flights that are scheduled to operate.
"These disruptions are unacceptable, and we call on Europe's Governments and the EU Commission to take urgent and decisive action to ensure that ATC providers are fully staffed and that overflights are not affected when national strikes take place, as they repeatedly do in France."
The complaints state that there is a legal precedent to this case.
In 1997, the Spanish complained to the European Commission when French farmers prevented their fruit and vegetable exports into the EU.
The European Court ruled against France as the French authorities did not address the farmers' actions and failed to ensure the free movement of goods.
According to Eurocontrol, more than 16,000 flights had been delayed by June this year due to air traffic control strikes, affecting more than two million passengers.