The slowdown at 40 of America's busiest airports is now in its third day and beginning to cause more widespread disruptions. That includes more than 7000 additional delays on Sunday, according to FlightAware, a website that tracks air travel disruptions.
More than 1000 flights were cancelled on Friday, and more than 1500 more on Saturday.
Transportation Secretary Sean Duffy warned that US air traffic could "slow to a trickle" if the shutdown if the federal government shutdown lingers into the busy Thanksgiving travel holiday season.
The Federal Aviation Administration last week ordered flight cuts at the nation's busiest airports as some air traffic controllers, who have gone unpaid for nearly a month, have stopped showing up for work.
The reductions started Friday at four per cent and will increase to 10 per cent by November 14. They are in effect from 6am to 10pm local time and will impact all commercial airlines.
Hartsfield-Jackson International Airport in Atlanta had the most cancellations on Sunday, with 173, followed by Newark Liberty International Airport in New Jersey, with 115.
The FAA said staffing shortages at Newark and LaGuardia Airport in New York were leading to average departure delays of about 75 minutes.
Detroit Metropolitan Wayne County Airport in Michigan was mostly empty on Sunday morning, with minimal wait times at security checkpoints as delays and cancellations filled the departures and arrivals boards.
Duffy has said additional flight cuts - perhaps up to 20 per cent - might be needed, particularly after controllers receive no pay for a second straight pay period.
"More controllers aren't coming to work day by day, the further they go without a pay cheque," he told Fox News.
And he prepared Americans for what they could face during the busy Thanksgiving holiday.
"As I look two weeks out, as we get closer to Thanksgiving travel, I think what's going to happen is you're going to have air travel slow to a trickle as everyone wants to travel to see their families," Duffy said.
With "very few" controllers working, "you'll have a few flights taking off and landing" and thousands of cancellations, he said.
"You're going to have massive disruption. I think a lot of angry Americans. I think we have to be honest about where this is going. It doesn't get better," Duffy said. "It gets worse until these air traffic controllers are going to be paid."
The government has been short of air traffic controllers for years, and multiple presidential administrations have tried to convince retirement-age controllers to remain on the job.
Duffy said the shutdown has exacerbated the problem, leading some air traffic controllers to speed up their retirements.
"Up to 15 or 20 a day are retiring," he told CNN.
Airlines for America, a trade group representing US carriers, said air traffic control staffing-related delays exceeded 3000 hours on Saturday, the highest of the shutdown, and that staffing problems contributed to 71 per cent of delay time.
From October 1 to November 7, controller shortages have disrupted more than four million passengers on US carriers, according to Airlines for America.
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