The national civil aviation authority says about one-tenth of flights were canceled Thursday because of the strike. At Paris' Orly Airport, most canceled flights were those heading to North Africa and southern France.
Air traffic controllers have held several strikes in recent years as the European Union has moved to streamline air traffic among countries that have already largely abandoned their land borders.
The plan will also mean government jobs lost, and workers say flight security may be compromised.
Baptiste Amiet, a CFDT union member striking at Orly Airport accused the EU's executive arm, the European Commission, of "fixing their performance goals only in terms of the cost."