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.
The FAA at one point asked that no new flight plans be filed.
The Associated Press contributed to this report