"It's going to be slow," Duffy told reporters at the White House, according to Reuters news agency.
More than 6,600 flights were canceled and 8,600 delayed, with another 1,500 already canceled for Sunday, according to FlightRadar24. Aviation analysts said the four-hour nationwide grounding could disrupt airline schedules for days.
Duffy said tens of thousands of passengers were stranded at airports around the country. Duffy said he and Homeland Security Secretary Markwayne Mullin had met with President Donald Trump in the Oval Office to discuss the outage.
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The failure 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 said the trouble began at 3:36 p.m., when air traffic control centers experienced instability in radar and communications systems.
"Our switches, our routers actually got overloaded with data and they started to give us inconsistencies in the data from those routers and because of that we shut the system down," Duffy said, adding that at no stage did they completely lose radar or communications and they were able to safely land thousands of planes.
$50 BILLION AVIATION OVERHAUL
Duffy blamed Congress for failing to fund a new system that he said could prevent such outages, and called for $50 billion to modernize it.
Earlier on Friday, before the outage, the White House and Department of Transportation had urged Congress to approve $30.1 billion to upgrade the nation's aging airports and air traffic control infrastructure.