The Federal Aviation Administration said the problem was fixed around 10 a.m., but it was unclear how long flights would continue to be affected. Doug Church, a spokesman for the National Air Traffic Controllers Union, said controllers were still entering flight plans manually in some locations.
FAA spokesman Paul Takemoto said the problem started between 5:15 and 5:30 a.m. and affected mostly flight plans but also traffic management, such as ground stops and ground delays. Airplane dispatchers had to send plans to controllers, who entered them into computers by hand.
"It's slowing everything down," Takemoto said.
Hartsfield-Jackson Atlanta International Airport, the world's busiest, has been particularly affected. Chicago and Washington, D.C., metro airports also reported delays due to the glitch.
Mary Rulo, an educator from Atlanta, was trying to get to Philadelphia for a conference. She said her 9 a.m. flight was delayed until 3 p.m. and AirTran was not able to help with other arrangements.
"This is really going to affect my conference schedule," she said. "It's really frustrating."
AirTran canceled at least 22 flights and dozens more flights were delayed as of 8 a.m. Delta Air Lines was also affected.
Passengers were asked to check the status of their flights online before going to airports.
Only minor delays were reported at metropolitan New York City area airports, according to the Port Authority of New York and New Jersey. Delays were also minimal at Logan International Airport in Boston. Orlando International Airport, Florida's busiest, reported about a dozen delays due to the chain reaction around the country, and flights in Tampa, Fla., were also delayed.
Flight plans are collected by the FAA for traffic nationwide at two centers -- one in the Salt Lake City area and the other in the Atlanta area. FAA spokeswoman Kathleen Bergen said she did not know which center was affected Thursday. Church said the computer failure involved both centers.
Victor Santore, the National Air Traffic Controllers Union southern region vice president, said he began getting e-mail messages from air traffic controllers around 7 a.m. EST Thursday that the Atlanta-area computers had stopped processing flight plans.
Santore said some controllers were pulled away from their normal duties talking to airplanes or pulled off breaks to help enter the flight plans.
"When something crazy like this happens, we'll pull everybody onto the floor," Santore said. "Every airport at some point some will be affected ... (The delays) are going to ripple through the entire system."
In August 2008, a software malfunction delayed hundreds of flights around the country.
In that episode, the Northeast was hardest hit by the delays because of a glitch at the Hampton, Ga., facility that processes flight plans for the eastern half of the U.S.
The FAA said at that time the source of the computer software malfunction was a "packet switch" that "failed due to a database mismatch."