"Normal air traffic operations are resuming gradually across the U.S. following an overnight outage to the Notice to Air Missions system that provides safety info to flight crews. The ground stop has been lifted. We continue to look into the cause of the initial problem" the FAA said in a Tweet.
The FAA had earlier ordered airlines to pause all domestic departures after its pilot alerting system crashed.
The FAA said shortly before 8:30 a.m. departures were resuming at Newark and Atlanta airports "due to air traffic congestion in those areas. We expect departures to resume at other airports at 9 a.m. ET."
The FAA is expected to implement a ground delay program in order to address the backlog of flights halted for hours. Flights already in the air were allowed to continue to their destinations.
U.S. President Joe Biden ordered the Transportation Department to investigate the outage and said the cause of the failure was unknown at this time. Asked if a cyber attack was behind the outage, Biden told reporters at the White House, "We don't know."
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 3,704 U.S. flights were delayed as of 8:39 a.m. ET, flight tracking website FlightAware showed. Another 656 were canceled as of 8:39 a.m.
Shares of U.S. carriers fell in Wednesday's premarket trading. Southwest Airlines was down 2.4%, while Delta Air Lines Inc(DAL.N), United Airlines(UAL.O)and American Airlines(AAL.O)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(UAL.O)said it had temporarily delayed all domestic flights and would issue an update when it learned more from the FAA.
Germany's Lufthansa and Air France both said they were continuing to operate flights to and from the United States, while the French airline said it was monitoring the situation.
The operator of Paris international airports - Paris Charles de Gaulle airport and Orly airport - said it expects delays to flights.
Austin-Bergstrom International Airport said on Twitter that ground stops across the country were causing delays. A ground stop is an air traffic control measure that slows or halts aircraft at a given airport.
In an earlier advisory on its website, the FAA said its NOTAM system had "failed", although NOTAMs issued before the outage were still viewable. Earlier this month, a problem with adifferent airline computercontrol system delayed dozens of flights in Florida.
A total of 21,464 flights are scheduled to depart airports in the United States on Wednesday with a carrying capacity of nearly 2.9 million passengers, data from Cirium shows.
American Airlines has the most departures from U.S. airports with 4,819 flights scheduled, followed by Delta and Southwest, Cirium data showed.