Airport authorities in Lyon, which has been hardest hit, said 30 percent of Monday morning's flights would be cancelled.
All morning flights were cancelled at Lyon's Saint-Exupery airport on Sunday while passengers at Paris' Roissy airport were waiting up to ninety minutes to clear security.
Security staff working for private company Brink's launched their action on Friday over a dispute concerning salary and working conditions.
Brink's attacked the "intransigence" of the strikers and accused them of "taking passengers hostage."
To cut waiting times, passengers were being advised not to bring unusually shaped bags to airports, such as skis or golf bags. Such bags "would not be loaded on-board," said an official at Lyon's airport.
Daily newspaper Metro reported the frustrations of many passengers who were kept waiting at the weekend.
"I've had to come here three times for nothing," said Myriam, waiting for a flight in Lyon. "The airline only told us about the cancellation a half-hour before departure."