American Airlines said it experienced “a system-wide network outage” Tuesday that affected its ability to access numerous computer systems, not just its reservation system.

The glitch grounded the airline’s network entirely for several hours and led to nearly 1,000 flight cancellations by American and regional affiliate American Eagle. The airline said its Sabre reservation system was not the problem, and Sabre emphasized its systems were “operating as normal … all day.”

In a video message posted on the airline’s website, American chairman, president and CEO Tom Horton apologized to the thousands of impacted passengers. “We had a software issue that impacted both our primary and back-up systems,” he explained.

The embarrassing snafu came just after American had filed its plan of reorganization to emerge from Chapter 11 bankruptcy protection, but that news was greatly overshadowed by the computer problems. US Airways chairman and CEO Doug Parker, who is slated to become the CEO of the new American following the pending US Airways-American merger, has said the combined carrier plans to use American’s systems.

American said it expected operations to return to near normal Wednesday.