Flight cancellations were again piling up on Monday as air traffic controller shortages, worsened by the longest-ever U.S. government shutdown, snarled air travel coast to coast while President Donald Trump threatened to dock air traffic controllers’ pay if they are absent from work.

On Monday, 2,079 of the 25,735 scheduled U.S. flights were canceled, just over 8% of the day’s schedule, according to aviation-data firm Cirium, which noted that on-time departures were better than average, though bad weather impacted airline operations as well.

Last week, the Trump administration ordered airlines to cut domestic flights at 40 major U.S. airports starting with 4% reductions last Friday and ramping up to 10% by this coming Friday, Nov. 14, citing strains on air traffic controllers.

“All Air Traffic Controllers must get back to work, NOW!!!,” Trump said in a post on Truth Social, adding that he would recommend $10,000 bonuses for any air traffic controllers who didn’t take any time off during the shutdown. He said those who don’t immediately return to work would be “docked.”

The National Air Traffic Controllers Association in response said that air traffic controllers are “unsung heroes, who report for duty to safely guide this country’s passengers and cargo to their destinations.” The organization said they “deserve our praise” and “have certainly earned it.” 

Disruptions over the weekend included 18,576 delayed flights while 4,519 were canceled, according to FlightAware. Cancellations spilled over from regional, short-haul jets — which the largest U.S. airlines rely on for around half of domestic flights — to mainline flying.

United Airlines and Delta Air Lines were each offering flight attendants extra pay to pick up flights, according to company messages seen by CNBC. United was also offering pilots extra pay for more flights than it usually does, an airline spokesman said. Such extra pay is common during storms or other disruptions.

American Airlines Chief Operating Officer David Seymour said Monday that 250,000 of its customers were affected by disruptions over the weekend, with 1,400 cancellations attributed to air traffic control.

“This is simply unacceptable, and everyone deserves better. Our air traffic controllers deserve to be paid and our airline needs to be able to operate at a level of predictability and dependability that no major airline was able to provide the flying public this weekend,” he said in a note to staff that was seen by CNBC.

Airlines were waiving change fees and in some cases, fare differences, depending on when customers could rebook travel. Customers could also request a full refund for the portion of their tickets they were unable to fly.

A sign of how severe air travel disruptions have become during the government shutdown: Sunday’s 2,631 U.S. flight cancellations, 10% of the day’s schedule, marked the fourth-worst day since January 2024, Cirium said.

In comparison, on Friday morning, as Trump administration-mandated flight cuts took effect, cancellations ranked 72nd since the start of last year.

The disruptions that upended the travel plans for hundreds of thousands of travelers forced them to look for alternative transportation. Car rental company Hertz last week reported an increase in one-way demand. There’s also been increased demand for private jet flights in recent days, according to the CEO of charter and fractional ownership company Flexjet.

Though the Trump administration order didn’t initially require private aviation to cut in the same way as commercial airlines, the Federal Aviation Administration on Monday began limiting those flights at a dozen U.S. airports. However, many private jet operators don’t use the busiest commercial airports, said the National Business Aviation Association.

The Senate made progress overnight on a deal that could end the shutdown, but it has not yet approved a funding bill.

Daniels said it isn’t yet clear how long it would take for controllers to receive back pay for their work. In the shutdown that ended in 2019, it took about 2½ months before the workers were made whole, he said.

Trump’s comments about air traffic controllers on Monday drew criticism from Rep. Rick Larsen, D-Wash., ranking member of the House Committee on Transportation and Infrastructure, who called the statement “nuts!” and said it ran counter to Transportation Secretary Sean Duffy’s call for aviation workers’ support.

“The women and men working long hours in air traffic control towers to keep the aviation system running deserve our thanks and appreciation, not unhinged attacks on their patriotism,” Larsen said.

An end to the shutdown also doesn’t mean that the flight restrictions will be lifted immediately. The FAA last week said it will determine whether to increase or decrease the flight restrictions based on safety data.

While airlines had little time to make the last-minute schedule changes when the order came out last week, to ramp up flying again they will need time to adjust schedules, sell seats and position planes and crews.

“Airlines’ reduced flight schedules cannot immediately bounce back to full capacity right after the government reopens. It will take time, and there will be residual effects for days,” Airlines for America, the lobbyist for the country’s biggest airlines, said in a statement late Monday. “With the Thanksgiving travel period beginning next week and the busy shipping season around the corner, the time to act is now to help mitigate any further impacts to Americans.”