"There are not any safety concerns or safety issues," she said.
Doug Church, a spokesman for the National Air Traffic Controllers Union, said controllers were still entering flight plans manually in some places even after the glitch was fixed, the Associated Press news agency reported.
New York City's John F Kennedy International Airport was operating at 40 to 50 per cent efficiency because of the glitch.
AirTran Airways said 38 flights were cancelled and dozens more were delayed nationwide because of the problem.
Delta Air Lines was also experiencing flight delays and cancellations, a spokeswoman said.
The delays were made worse by inclement weather in the Northeast, with airports in the Chicago, Washington, DC, and New York metropolitan areas reporting disruptions.