A key process, it said, had been "impaired" in an outage of its Notice to Air Missions system (NOTAM), which provides information to flight crews about hazards, changes to airport facilities and other essential information.
The pause, it said, would allow "the agency to validate the integrity of flight and safety information."
Speaking to reporters, President Joe Biden said that he had been briefed by the transportation secretary and that "aircraft can still land safely, just not take off right now."
"They don't know what the cause of it is, they expect in a couple of hours they'll have a good sense of what caused it and will respond at that time," Biden said.
"The FAA is still working to fully restore the Notice to Air Missions system following an outage," the agency said in a statement, adding that while "some functions are beginning to come back on line, National Airspace System operations remain limited."
Thousands of delayed flights
White House Press Secretary Karine Jean-Pierre tweeted that "there is no evidence of a cyberattack at this point."
"The President directed DOT to conduct a full investigation into the causes. The FAA will provide regular updates," she said, referring to the Department of Transportation.
There were at least 3,700 flights delayed in the United States by 8:30 am US Eastern time (1330 GMT), flight tracking website Flight Aware data showed.
American Airlines said that it was "closely monitoring the situation, which impacts all airlines, and working with the FAA to minimize disruption to our operation and customers."
Transportation Secretary Pete Buttigieg said he was in contact with the FAA.
"I have been in touch with FAA this morning about an outage affecting a key system for providing safety information to pilots," he tweeted.
"FAA is working to resolve this issue swiftly and safely so that air traffic can resume normal operations, and will continue to provide updates."
The halt comes in the wake of a large-scale aviation meltdown in the United States over the Christmas holiday, as a storm brought unseasonably cold temperatures to the majority of the country and caused chaos, with thousands of flights delayed or canceled.
Hard-hit Southwest Airlines canceled more than 15,000 flights over eight days after what it said was a breakdown in its scheduling systems.