The action began with just one controllers union but quickly spread to members of the European Transport Workers Federation, Radio France Internationale reported Wednesday.
The dispute centers on the European Commission's Single European Sky plan to integrate air traffic management systems across the continent.
Strikers agreed to end their three-day action after only two days because the French and German governments have called on the commission to drop privatization proposals from the plan.
The strike is causing delays as long as nine hours for passengers as flights are diverted onto alternative routes, the British newspaper The Daily Telegraph reported.
British Airways is among the airlines forced to cancel a number of flights along with Easyjet and Ryanair.
A Eurostar spokesman said passengers are switching to rail.
On Tuesday, tourists from all over the world arrived at Charles de Gaulle airport in Paris to find themselves unable to make connecting flights, The New York Times reported.
Many passengers said they could not comprehend why France appeared so resistant to changes that economists said have the potential to bolster travel and economic growth.