Of 4,500 scheduled flights, only 502 were expected to take off. The strike was also expected to cut in half the scheduled 3,000 flights over French airspace, according to the General Direction for Civil Aviation.
The 24-hour strike was to end Tuesday morning. A few controllers were working despite the strike.
It was the first general work stoppage in nearly a decade by air traffic controllers. The National Union of Air Traffic Controllers and all other controllers' unions were protesting what they say are plans by the EU to privatize the industry.
Many European carriers were forced to cancel flights to France and reroute planes that would normally fly over the country.
Finnair and Scandinavian Airlines, the multinational airline for Denmark, Norway and Sweden, canceled all flights to France. Spain's state airline, Iberia, canceled 26 flights and Swissair and Crossair, a regional Swiss airline, canceled 120 flights on Monday.
Other flights averaged 90-minute delays, with flights to southern Europe rerouted via Italy, and trans-Atlantic flights diverted to German airspace.
The state-run train authority said it provided 5,000 extra seats over the weekend to help compensate for canceled flights between Paris and major French and other European cities.
European Transport Commissioner Loyola de Palacio is seeking to replace national management systems of the crowded skies with a joint management program.
Loyola was to present European transport ministers with a draft report of her "single skies" plan on Monday.
She has estimated that increased flight delays cost some $5 billion in 1999.
France's Transport Minister Jean-Claude Gayssot said in statement: "Each state should remain free to organize its own system."