"Several airlines are experiencing issues with a flight planning weight and balance program," the FAA said in a statement after Delta and Southwest reported issues via Twitter. United, JetBlue and Alaska Airlines were also affected by the computer outage, as well as American Airlines regional carriers, the FAA said.
Aerodata, the system which went down, is used by the airlines use to check the weight and balance of planes before takeoff. Aerodata has not yet responded to ABC News' requests for comment.
Planes were grounded nationwide, including in Los Angeles, New York and Chicago, but systems for at least three of the major airlines were resolved within about an hour. The rest of the impacted airlines resolved the issue in the following hours.
Delta, Southwest and American each reported the computer system issue was resolved before 8:30 a.m. and Southwest reported its ground stop was lifted within 40 minutes. Both Delta and Southwest said the outage caused delays but not cancellations. The short time down was not predicted to cause major ripple effects for travel Monday, but had the largest effect on Southwest flights.
Twenty-two percent of Southwest flights were delayed Monday, according to the live flight-tracking website FlightAware, while other airlines saw delays in the ballpark of 2 to 5 percent.
Most of the airlines apologized to passengers and asked for patience in response to grievances aired on Twitter, saying they were working to reduce the impact of scattered delays.
"A brief third-party technology issue that prevented some Delta Connection flights from being dispatched on time this morning has been resolved. No cancellations are expected due to the issue and our teams are working to resolve some resulting delays," Delta said in a statement.
"The technical issue that impacted a few of our regional carriers has been resolved. We apologize to our customers for the inconvenience," American Airlines responded to passenger complaints on Twitter.
"We’re working with Customers on any impacts to their travel plans and we appreciate their understanding as we place nothing higher than the safe operation of every flight," Southwest said in a statement.
Monday morning's computer issues come after several airlines of the same airlines suffered another outage to a different system last week. The Sabre system, which handles ticketing and boarding, affected American, JetBlue and Alaska Airlines.
ABC News' David Kerley and Jeffrey Cook contributed to this report.