The U.S. has been scrambling to hire more air traffic controllers for years. The longest-ever federal government shutdown might have made that even harder.

“We need more of them to come into the profession, and this shutdown is going to make that more difficult for us to accomplish that goal,” Transportation Secretary Sean Duffy said at a press conference at Chicago O’Hare International Airport on Tuesday, a day before Congress signed a bill to fund the federal government through January, ending the shutdown.

Air traffic controllers were required to work without receiving regular paychecks during the shutdown. They were paid in part on Friday, according to people familiar with the matter, but during the shutdown some had taken second jobs to make ends meet, while the lack of regular pay added to their stress, union and government officials and lawmakers have said.

The Federal Aviation Administration reported low-staffing thresholds were hit that that slowed aircraft around the country during the final days of the shutdown. President Donald Trump earlier this week threatened to dock air traffic controllers’ pay if they didn’t go to work. On Friday, staffing levels were relatively strong around the U.S. and disruptions eased.

“It can’t make it look like this is a great job because you’re going to have to deal with this all the time,” said Tim Kiefer, who teaches air traffic management at Embry-Riddle Aeronautical University in Prescott, Ariz.

Kiefer was an air traffic controller for more than two decades before he retired. He said shutdowns or the threat of them were common during his career. “You may see people decide to do other things and say, ‘They didn’t get paid; they were stuck in the middle of a partisan dispute,'” he said.

The shortage of air traffic controllers delayed or canceled thousands flights during the shutdown, affecting the travel plans of more than 5 million people, according to Airlines for America, an industry group that includes American Airlines, United Airlines, Delta Air Lines, Southwest Airlines and others.

But even with partial pay hitting bank accounts, the staffing crisis that regularly upends travel is set to continue.

A government tally last year showed the U.S. was short 3,903 fully certified air traffic controllers of a goal of 14,633. Shortages have been particularly severe at busy facilities like those where controllers guide planes in and out of airports in the congested New York area, adding to flight disruptions and frustrating airline executives and customers.

Meanwhile, retirements picked up in the shutdown, with 15 to 20 people retiring per day, down from a usual rate of four a day, Duffy said Tuesday. Controllers are required to retire at age 56 but can do so earlier with benefits depending on years on the job.

Staffing was already thin before the shutdown began on Oct. 1, and many controllers were working six-day workweeks. By mid-November, as air traffic controllers missed two full paychecks and the shutdown passed the one-month mark, it approached crisis levels.

More than 10% of U.S. departures were canceled last Sunday as bad weather combined with air traffic controller shortfalls at facilities across the country. That was the highest rate since July 19, 2024, during the CrowdStrike outage, which had an outsize impact on Delta Air Lines, leading to thousands of canceled flights and causing travel headaches, according to aviation-data firm Cirium.

Hours after those cancellations spiked on Sunday, the Senate advanced a preliminary deal that led to the vote ending the shutdown this week.

The Federal Aviation Administration in early November ordered airlines to cut 4% of flights from their domestic schedules at 40 major airports, blaming safety risks they found because of an increased strain on air traffic controllers. Cuts were set to ramp up to 10% on Friday, if the shutdown didn’t end. Cancellations, however, improved dramatically during the week and on Friday morning, just 2% of U.S. departures were canceled, according to Cirium.

The FAA brought its mandated cuts down from 6% to 3% starting on Saturday, saying it will monitor system performance throughout the weekend.

The disruptions were similar to those on days with severe storms, but were more widespread across the U.S.

The last-minute cuts were a headache for the industry, where airlines from top-moneymaker Delta to struggling carrier Spirt had already lowered their outlooks for the year after an oversupply of flights and weaker-than-expected demand earlier this year. Airlines haven’t yet quantified the damage from the shutdown, but Bank of America estimated a $150 million to $200 million operating income hit for big network airlines and less than $100 million for other carriers.

Airline executives, exasperated by the recent disruptions, are now pushing Congress to make sure controllers are paid in the next shutdown.

“In the past week, we saw a crescendo effect as air traffic control staffing shortages led to massive and unpredictable amounts of delays and cancellations across the industry — and that was on top of a series of FAA-mandated schedule reductions,” American Airlines CEO Robert Isom and the carrier’s chief operating officer, David Seymour, said in a note to employees on Thursday, a day after the House approved a short-term funding bill. “While we both have been in this industry for a long time, only a few other events come to mind when we think about this level of disruption.”

It could have been worse. This part of the fall travel demand is relatively light, but Thanksgiving was fast approaching when Congress ended the shutdown, concerning airline executives.

“This shutdown put tremendous strain on our aviation system and caused severe inconvenience for the millions of Americans who depend on it,” United said in a statement. “It should be obvious to everyone that policy debates, however urgent, should never put air travel at risk, and we urge Congress to ensure that the FAA and [Transportation Security Administration’s] funding is protected in the event of any future lapse in federal appropriations.”

Delta CEO Ed Bastian told CNBC’s “Squawk on the Street” on Wednesday that “the thing we don’t like is being a political football” and said it was unacceptable that air traffic controllers and TSA officers were forced to work without regular paychecks.

The best way to prevent such disruptions is “to ensure those workers, the next time this happens because it will happen, get paid,” Bastian said. “Who could disagree with that?”

The airline industry is urging Congress for legislation that could make use of funds generated by airplane ticket taxes to ensure air traffic controllers and other essential industry workers like airport screeners and Customs agents are paid.

“You don’t hold the American public hostage over a political fight like that,” Airlines for America CEO Chris Sununu, the former governor of New Hampshire, said in a virtual press conference Wednesday, shortly before the House passed the funding bill.

Next Wednesday, Sen. Jerry Moran, R-Kan., who chairs the Commerce Subcommittee on Aviation, Space and Innovation, will hold a hearing on the shutdown’s impact on aviation. Moran this year pushed for legislation that would let the FAA use the Airport and Airway Trust Fund, which is funded by taxes on airplane tickets and fuel, to cover expenses if the government shuts down.

“The government shutdown has severely impacted our already fragile aviation industry, and recovering from its effects will take time,” he said in a release this week. “It’s critical that we address the damage done and look at the long-term effects of the shutdown.”

Lawmakers earlier this year approved $12.5 billion to improve air traffic control, though the industry said it needs billions more to modernize the system in the U.S.

The fatal collision of an American Airlines regional jet and an Army Black Hawk helicopter in Washington, D.C., in January also made hiring controllers more urgent, especially at congested facilities.

About a month after the crash, Duffy announced the country’s air traffic controller academy would raise pay for students, and he authorized more universities to teach a similar curriculum to help ease the shortage. The academy in Oklahoma City also stayed open, a different tactic than in the 2018-2019 shutdown.

But those aren’t immediate fixes. It takes years for controllers to be fully trained to work at some of the more complex facilities, and applicants to the academy can be no older than 30.