The Civil Aviation Authority said that some 1,800 flights were cut Tuesday in Charles de Gaulle, Orly, Beauvais, Lyon, Nice, Marseille, Toulouse and Bordeaux airports.
More than 300 budget airline flights scheduled to travel through French airspace were cancelled on Wednesday.
Worst affected were Orly and Charles de Gaulle, the two Paris hubs, and Nice, the main airport for the French Riviera.
The European Transport Workers' Federation said air traffic workers in 11 European countries were taking action Wednesday to voice their opposition to plans involving a single European airspace.
France has asked Brussels to review the plans, a move which prompted the unions to cancel a third day of strike action that had been scheduled for Thursday, when more than half of France's trains will not be operating.
Eurostar services from Paris to London and high-speed links to Belgium, The Netherlands and Germany were not expected to affected by the strike but one in two trains to Switzerland and one in three to Italy were set to be cancelled.