Airlines in the United States have cancelled more than 3,300 flights amid a top transport official’s warning that air travel could “slow to a trickle” due to the ongoing government shutdown.

The cancellations on Sunday came as Republicans and Democrats reached a stopgap deal to end the shutdown after the impasse over the passage of a funding bill dragged into its 40th day.

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Travel disruption has been mounting since the Federal Aviation Administration (FAA)  last week ordered reductions in air traffic amid reports of air traffic controllers exhibiting fatigue and refusing to turn up for work.

Some 13,000 air traffic controllers, who are deemed “essential” employees under US government rules, have been forced to work without pay since the start of the shutdown on October 1.

A total of 3,304 US flights were cancelled and more than 10,000 flights were delayed on Sunday, according to data from flight-tracking website FlightAware.

More than 1,500 flights were cancelled on Saturday, following the cancellation of about 1,000 flights on Friday.

Under the FAA’s phased-in reduction in air traffic, airlines were ordered to reduce domestic flights by 4 percent from 6am Eastern Standard Time (11:00 GMT) on Friday.

Flights are set to be reduced by 6 percent from Monday, 8 percent by Thursday, and 10 percent by Friday.

In media interviews on Sunday, US Secretary of Transportation Sean Duffy warned that air travel could grind to a standstill in the run-up to the Thanksgiving holiday on November 27.

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“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 told Fox News.

“It doesn’t get better,” Duffy added. “It gets worse until these air traffic controllers are going to be paid.”

The period around Thanksgiving is one of the busiest times for travel in the US calendar.

An estimated 80 million Americans travelled during the Thanksgiving period in 2024, with airports screening a record 3.09 million passengers on the Sunday after the holiday alone.

As fears of travel chaos mounted on Sunday, US senators said they had reached a compromise agreement to restore funding for government operations through the end of January.

The Senate on Sunday night began a procedural vote to move the package forward after several moderate Democrats said they would join Republicans to support the resumption of government funding.

The funding plan will still need to be approved by the Senate and the US House of Representatives, and then signed into law by US President Donald Trump, to bring the shutdown to an end.

It is also unclear whether travel disruption could persist after the government reopens.

The FAA said last week that decisions on lifting its flight reductions would be “informed by safety data”.

Al Jazeera has contacted the FAA for comment.

Richard Aboulafia, managing director at the consultancy AeroDynamic Advisory, said that if air traffic controllers have been skipping work due to pay, the disruptions should quickly dissipate once the shutdown ends.

But Aboulafia also said that he and others have suspicions that the flight restrictions are an “arbitrary slowdown designed to exert political pressure”.

“The decision to restrict capacity was understandable if the facts and data support it,” Aboulafia told Al Jazeera.

“Secretary Duffy says the data does indeed support it, but he has not shared any of that data. People are right to be suspicious, particularly in light of other unnecessary cuts by the administration.”