The powerful SNCTA union called the two-day strike, saying the government has refused to open negotiations about matters such as how to better organize their work schedules to account for downtime and more traffic.
The start of the walkout led to the cancellation of 40 per cent of flights across France on Wednesday, and the French civil aviation agency called for the cancellation of 50 per cent of flights on Thursday due to staffing shortages.
Air France said long-haul flights were not affected, and guaranteed some 60 per cent of medium-haul flights from and to Paris' main airport, Charles de Gaulle. The carrier said it would ground two of three flights at Paris' second-largest airport, Orly.
Among other things, strikers are protesting against government plans to increase the maximum retirement age for air traffic controllers from 57 by 2017 to 59 in 2020, said Nicolas Bertolissio, an SNCTA representative and a controller in the Basel-Mulhouse airport in eastern France.
While the union isn't altogether opposed to that, it wants a study into the health effects of controllers working till age 59, Bertolissio said.
He said many other countries in Europe generally allow for traffic controllers to retire at 55 or 56.
The strike caused passengers like Mathias Mourier, 24, who was trying to fly to his job in southern England as an au pair, to scramble for alternatives. He said he will be spending an extra couple of nights at his grandmother's house in the Paris region.
"I was about to get my flight to go to Exeter ... and finally it was cancelled because of the strike," he said at Paris' Roissy airport. "So I have to wait until Saturday because all the other flights were full ... It is the only solution."
Jackie Knight, who was hoping to return home to Somerset, England, after a family visit to Disneyland Paris, said they were forced to connect through London, but was taking it in stride.
"Rather than being home at about 3 or 4 (p.m.), it will be in the evening — but we'll get there," she said.
Further strikes are planned April 16-18 and April 29-May 2, coinciding with spring school holidays in France.