But by early evening, the FAA said that the situation around the country was returning to normal, with delays remaining in Atlanta and Chicago.
CBS News correspondent Bob Orr reported that by early evening, the FAA "identified the basic problem with the computer system" in Atlanta and was "in the process of restoration now." An agency spokesman told Orr the problem appeared to be an "internal software processing" problem.
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."
The FAA said the glitch appeared to have involved a software problem.
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.
She said she did not know exactly how many flights were affected, but she said it was in the hundreds. The FAA did not expect to have total figures until Wednesday. Bergen said that in a 24-hour period the FAA processes more than 300,000 flight plans in the U.S.
Bergen said the problem that occurred Tuesday afternoon involved an FAA facility in Hampton, Ga., south of Atlanta, that processes flight plans. She said there was a failure in a communication link that transmits the data 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. FAA spokeswoman Diane 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, though the Hampton facility was not yet processing flight plans again.
"We have our engineers looking at it and we're doing a complete investigation," she said.
She said delays of 30 minutes remained at airports in Chicago while delays of 60 minutes remained in Atlanta, which was also experiencing weather issues.
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 immediately 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 it was easing up by early evening.
Carolyn Fennell, spokeswoman for the Orlando International Airport, said 13 Southwest Airlines flights had been affected by the glitch.
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.