The Northeast was hardest hit by the delays prompted Tuesday by a glitch at a Hampton, Ga., facility that processes flight plans for the eastern half of the U.S.
An agency spokesman told CBS News correspondent Bob Orr the problem appeared to be an "internal software processing" problem.
As of Wednesday morning, the FAA said that the situation around the country had returned to normal, with most delays from the malfunction being cleared up Tuesday night. But spokeswoman Diane Spitaliere said the investigation into what caused the problem is still ongoing, and she did not know when it would be completed.
"It usually takes a while to be quite honest," she said.
The glitch has illustrated how easily a single, seemingly isolated snafu can trigger disarray across in the country's aging air-traffic system.
The FAA says the problem yesterday delayed around 650 flights in the East and Midwest, including Chicago.
The chief operations officer for the U.S. air traffic system, Hank Krakowski, says the computer is now operating normally. But he says yesterday's disruptions were frustrating.
He says it shows that just upgrading the network piecemeal isn't good enough. He says what's needed is whole-scale modernization.
The air traffic controllers union says it also supports modernization. But it accuses the FAA of being too fixated on future technology and of not maintaining existing equipment well enough.
At one point, an FAA Web site that tracks airport status showed delays at some three dozen major airports across the country. The site advised passengers to "check your departure airport to see if your flight may be affected."
Sen. John McCain, the Republican presidential candidate, said the episode "once again highlights the need to reform and repair a broken system." His Democratic rival, Sen. Barack Obama, said "airline passengers are sick and tired of delays and cancellations." And the nonprofit Travel Industry Association called it "one more example of America's deteriorating air travel system."
The FAA, for its part, said it would work to make sure the problem doesn't happen again.
Another FAA spokeswoman, Kathleen Bergen in Atlanta, said there were no safety issues and officials were still able to speak to pilots on planes on the ground and in the air.
According to the FAA, 646 flights had been delayed as a direct result of the problem. In a 24-hour period the FAA processes more than 300,000 flight plans in the U.S., the agency said.
Bergen said the problem that occurred Tuesday afternoon involved a failure in a communication link that transmits flight plan data from the Georgia facility to a similar facility in Salt Lake City.
As a result, the Salt Lake City facility was having to process those flight plans, causing delays in planes taking off. She said the delays were primarily affecting departing flights. Spitaliere said there were some problems with arriving flights as well.
During an early evening conference call with reporters, Spitaliere said Tuesday's glitch appeared to be a software problem and the situation was returning to normal. The Hampton facility began processing flight plans again as of 1:15 a.m. Wednesday, Bergen said.
As of Tuesday evening, airports in Chicago were still experiencing 30-minute delays, while delays of 60 minutes were seen in Atlanta, which also dealt with weather issues. Bergen said those delays were cleared up as of Wednesday morning.
Bergen said there was an unrelated hardware problem at the Hampton facility on Aug. 21 that resulted in issues processing flight plans. The FAA says on its Web site that a glitch that day involving the Hampton facility delayed the departure of at least 134 flights.
A spokesman for Hartsfield-Jackson Atlanta International Airport, the world's busiest airport, did not return a call seeking comment on the impact there from Tuesday's episode. Bergen said officials at the Atlanta airport were entering flight data manually to try to speed things up.
Discount carrier AirTran Airways, which has its hub at the Atlanta airport, said in a statement that because of the suburban FAA center snafu it was at one point taking up to an hour for the FAA to get clearances to the towers for departures Tuesday. Delta Air Lines Inc., which has its main hub in Atlanta, said flights were processing for takeoff, but slowly.
The communication failure caused delays for departures and arrivals at Baltimore-Washington International Thurgood Marshall Airport, according to airport spokeswoman Cheryl Stewart. However, she did not have a number on delays.
The FAA at one point asked that no new flight plans be filed, Stewart said.
Phil Orlandella, a spokesman for Massport, which operates Boston's Logan International Airport, said there were significant delays there, but the situation eased up by Tuesday evening.
The National Airspace Data Interchange Network is a data communications system for air traffic controllers. It's used to distribute flight plans and allows controllers to know when planes are leaving, where they're going and other details.
Allen Kenitzer, a western regional spokesman for the FAA, said the Utah system could handle the extra load while workers tried to get the Atlanta area system back online, but it was expected to slow down air traffic.
"We're not going to let an unsafe condition exist. It's just going to be slower," Kenitzer said.