United Airlines planes grounded at Newark International Airport, in Newark, New Jersey, during the outage. Photo: AFP
Normal air traffic operations are slowly resuming in the US after hours of delays, the Federal Aviation Administration (FAA) says.
It follows a problem with the system that alerts pilots to potential hazards on flight routes.
The FAA had said flights would begin to take off again from 9am US ET, though further delays were expected due to backlog of flights.
Flights already in the air were allowed to continue to their destinations.
As of Wednesday morning, more than 5800 flights in and out of the US had been delayed and more than 800 were cancelled. Airports across the country were affected, from Denver to Atlanta to New York City.
"This technology issue is causing significant operational delays across the national airspace system," said Airlines for America, an industry group that represents major US airlines like Delta, American and United.
Flight operations began to resume later in the morning, though major airlines said further delays are expected to address the backlog of flights that had been halted for hours.
One issue airlines were facing was trying to get planes in and out of crowded gates, which was causing further delays.
US President Joe Biden has been briefed, and the White House said there was no evidence of a cyberattack "at this point".
Speaking to reporters, the president said the FAA "expect [that] in a couple of hours they'll have a good sense of what caused it, and we'll respond at that time".
In a tweet, the White House press secretary said the president had called for a "full investigation".
The FAA said the source of the problem was its notice to air missions system.
Major US airlines said they were closely monitoring the situation. American Airlines, which carries the most passengers annually in North America, said it was working with the FAA to minimise customer disruption.
Travellers wait in the terminal for their flights at Ronald Reagan Washington National Airport in Arlington, Virginia. Photo: AFP / Saul Loeb
United Airlines said it would waive change fees and any difference in fare for customers rescheduling flights departing on or before Monday.
Delta said it was "safely focused on managing our operation during this morning's FAA ground stop for all carriers", adding it would provide updates as soon as possible.
For international passengers, Air Canada - the foreign carrier with the most flights into the US - said the outage would impact on cross-border operations on Wednesday, but it couldn't initially say to what degree. The carrier said it would put in place a "goodwill policy" so affected passengers can change their travel plans.
Meanwhile, airports in Paris - Paris Charles de Gaulle and Orly - said they expected delays to US flights. Air France said it was monitoring the situation.
For UK passengers, British Airways said its flights to and from the US will operate as planned, and Virgin Atlantic said it was continuing to operate its schedule of US flights departing from the UK. However, some US departures, the airline said, may be affected by delays.
Germany's Lufthansa and Spain's Iberia said they were still operating flights to and from the US as normal for now.
US Department of Transportation Secretary Pete Buttigieg said he had been in contact with the FAA on Wednesday morning, and that they were working to resolve the issue "swiftly and safely".
Passengers have posted on social media that they are experiencing delays.
"Always great to get up at 0400 to be at the gate in plenty of time for your flight that is now delayed by 37 minutes and counting," said Daniel Huard in a Facebook post. "This will be a long day of travel."
Michael Remy arrived to an airport in Virginia at 6am planning to head to North Carolina for a vacation. His flight was delayed right before boarding. "It is what is, so, you can only get so upset," he told the BBC. "I may have seen it differently if I was headed to a wedding or a funeral, though."
-BBC