Flights already in the air were allowed to continue to their destinations.
The FAA said it was working to restore a system that alerts pilots to hazards and changes to airport facilities and procedures that had stopped processing updated information.
"The FAA is still working to fully restore the Notice to Air Missions (NOTAM) system following an outage. While some functions are beginning to come back on line, National Airspace System operations remain limited," the FAA said on Twitter.
A total of 1,230 flights were delayed within, into or out of the United States as of 7.19 am ET (1219 GMT), flight tracking website FlightAware showed, without citing reasons. Another 103 within, into or out of the country were also canceled.
Shares of U.S. carriers fell in Wednesday's premarket trading. Southwest Airlines was down 2.4%, while Delta Air Lines Inc, United Airlines and American Airlines were down about 1%.
A NOTAM is a notice containing information essential to personnel concerned with flight operations, but not known far enough in advance to be publicized by other means.
Information can go up to 200 pages for long-haul international flights and may include items such as runway closures, bird hazard warnings and construction obstacles.
United Airlines said it had temporarily delayed all domestic flights and would issue an update when it learned more from the FAA.
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