PARIS—A French-led strike to protest against plans to reform Europe's fragmented air-traffic control system disrupted travel Tuesday, with half of flights to and from Paris's main airport canceled as well as some flights from other major European hubs such as London and Frankfurt.

But the French trade union leading the protest called off the third day of its promised strike action after the French government publicly criticized the European Commission, the European Union's executive arm, for its latest attempt to reform the...