Following four days of disruption, the controllers had suspended their go-slow for eight hours, allowing airlines to catch up on their schedules, airport officials said.
One air traffic controller, who asked not to be named, said they were clearing one plane to land or take off every 15 minutes.
But on Friday, some planes were delayed up to five hours, the airport officials said.
At least four air traffic controllers have been dismissed in the dispute. Civil Aviation Minister Ahmed Shafiq threatened more dismissals if the go-slow continued.
"I've ordered an immediate inquiry into the reasons ... . If anyone is proved to be involved, he will be dismissed immediately because there can be no leniency for anyone who causes big losses to Egyptian and foreign companies," he said.
An official of the state carrier EgyptAir said the company had lost $2 million in two days, besides the extra cost of feeding passengers and putting them up in hotels.
The Egyptian authorities have waived landing fees for airlines to compensate them for the delays.
The controllers want their salaries doubled over three years, better health insurance and other improvements, the air traffic controller said. Shafiq has said that after recent increases, they have no reason to complain.
Hands-on controllers earn 3000 Egyptian pounds ($520) a month and will receive raises of up to 600 pounds a month from this month, the controller said.