In a conference call with reporters, the FAA said the problems began when an Atlanta facility that processes flight plan information went down due to a software malfunction.
Once that facility went down, the information was sent to a backup facility in Salt Lake City. But the Utah facility was quickly overloaded as multiple airports re-filed their flight plans, leading to delays.
The failure did not lead to radar outages, or communication issues with in-flight planes, FAA spokesperson Kathleen Bergen said. The problem only affected planes that were waiting to take off.
The delays began shortly after 1 p.m. EST and airports in Chicago, Atlanta, Boston, and Washington D.C. were hardest hit.
The FAA's computer system is the National Air Space Data Interchange Network, or NADIN, and officials ruled out terrorism or hacking as the cause of the problem.
"It appears to be an internal software processing problem," said Hank Krakowski, CEO for the FAA's air traffic division, in a conference call. "We're going to have to do some forensics on it."
But Krakowski added that the failure in Atlanta was "unprecedented," and that the agency needs to analyze it to understand it. The NADIN software is expected to be upgraded by the end of the year, but officials did not say how it would improve the current system.
The FAA said it expects to have the problems solved by Tuesday night, and for now, the Salt Lake City facility is now process all of the nation's flight plan information.