As of 6:45pm on Saturday (10:45 AEDT Sunday), airlines had cancelled more than 6,150 US flights and delayed more than 7,300, according to FlightAware, an aviation website.
That followed about 9,200 flights cancelled and 7,500 delayed on Friday after the FAA ordered a nationwide ground stop because of disruptions to air traffic communications. FlightAware said more than 530 flights scheduled for Sunday were already cancelled.
Federal Aviation Administration head Bryan Bedford said on Saturday he expected airline operations to largely return to normal by late on Sunday and apologised for the disruption.
The FAA issued a nationwide ground stop on Friday that halted nearly all departing flights for almost five hours. It was the longest nationwide halt to air travel since the attacks of September 11, 2001 and one of the single worst US travel days ever.
The issue prompted the White House to convene an emergency meeting in the Situation Room on Friday and federal agencies to scramble to determine if it was a cyberattack. But the problem was traced to FAA contractor L3Harris' installation of at least one new router at a remote facility, Transportation Secretary Sean Duffy said on Saturday.
"We're working to determine whether we had incompetence, meaning was it user error or installer error from L3Harris, or did they install a faulty router? We haven't determined what the fault was," Duffy told reporters at a news conference.
L3Harris said it took the issue seriously and is supporting the FAA in its investigation. Its shares last traded down about four per cent after hours on Friday.
Duffy said the trouble began on Friday afternoon, when air traffic control centres experienced instability in radar and communications systems. The router issue led to data overloading other communications centres, officials said.
"We had over 1,000 connection attempts every four to five seconds, and what that did was (it) gave us issues with our communication with airplanes, and it also caused some disruption with our radar," Duffy added.
The issue affected communications at 17 of the FAA's 22 en route centres, which control aircraft during the cruise portion of a flight. Bedford said the FAA ordered the ground stop in case a centre lost all communications. "No facilities went dark. Nothing was fully lost", Bedford added.
The FAA said it was doing additional testing with L3Harris to see if there are any additional risks.
Delta Air Lines, United Airlines and American Airlines all cancelled about 25 per cent of their flights on Saturday, while JetBlue cancelled nearly 45 per cent. Airlines have issued travel waivers allowing passengers to rebook flights for later dates without cost.
Though the FAA lifted the ground stop on Friday evening, the disruption for passengers was far from over, with tens of thousands of people stranded in airports. Airlines were trying to get flight crews and other personnel in position to resume flights.
Friday's disruption is the latest and most dramatic sign of strain on a US air traffic control system beset by aging technology, equipment and communications problems and a shortage of several thousand controllers.
Duffy called on Friday for $US50 billion ($A74 billion) in funding to upgrade air traffic control systems, up from his earlier request of $US30 billion ($A44 billion) - after Congress approved $US12.5 billion ($A18.5 billion) in 2025.
