US Transport Secretary Sean Duffy blamed the stoppage on what he called an "incredibly old" air traffic control system and warned that it would take time for normal operations to resume.
Passengers travelling to and from the United States continue to face delays and cancellations to flights on Saturday morning despite the Federal Aviation Administration (FAA) having lifted a nationwide ground stop.
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The rare order had been issued on Friday following a "telecommunications outage," with all flights halted across the country.
The FAA has since lifted the ground stop and said that some flight departures were resuming.
"Before clearing flights to resume, we thoroughly tested our systems to confirm they were stable and that operations remain reliable," the agency said, while advising travellers to contact airlines for flight updates.
US Transport Secretary Sean Duffy blamed the stoppage on what he called an "incredibly old" air traffic control system and warned that it would take time for normal operations to resume.
"At 8:15 (pm) tonight, eastern time, we've opened up the airspace. Now does that mean every flight is going to fly? Right now, it's going to be slow," he told reporters. "It depends on do we have crews available, do we have pilots and flight attendants available to fly your flight. We're going to try to move as many of those as we can tonight."
"But it's going to take us some time to unwind what's happened," he added.
Flight-tracking site Flightradar24's airport disruption map shows major problems at airports across the US on Saturday morning.
FlightAware, another tracking service, put the number of cancellations to flights to or from the US on Friday at more than 8,860. It said around 2,650 more have been cancelled so far on Saturday.
United Airlines, Delta and American have all said they are resuming flight operations.
"We're focused on operating as many remaining flights as possible this evening while positioning the airline for the strongest possible recovery in the days ahead," American said in a statement late on Friday.