QUEENS, N.Y. — At John F. Kennedy International Airport in New York City this Thursday, travelers queued at TSA checkpoints, anxious to get to their gates before their flights took off.

At Terminal 4, which serves mostly Delta (DAL) and some international carriers, the lines for TSA Pre-check, digital ID, and Clear — the private screening company — were surprisingly quick; however, general TSA lines appeared to have wait times of around 30 minutes.

“We left four hours earlier than we originally planned,” Mike Mayer, an aviation and defense executive based in New York, said after he got through security in Terminal 4.

But right next door at Terminal 5, which serves budget airline JetBlue (JBLU), wait times for general boarding appeared to last for hours.

While it worked out fine for Mayer, and he got through security with plenty of time, it’s been a disaster everywhere else, and he felt the pain for TSA workers.

“I think it’s a travesty they’re not getting paid,” he said.

Read more: CLEAR+ lets you bypass TSA checkpoints for ID. Is it worth the cost?

With the government shutdown extending beyond 40 days, TSA workers have now missed two paychecks, leading to more workers than usual calling out. Add that to the 480 workers who quit their jobs during this shutdown and the shortage of trained TSA workers at airports, and it’s leading to closed security checkpoints, multiple-hour waits in security lines, and missed flights.

Reports from Baltimore’s BWI Airport, Houston’s George Bush Intercontinental Airport, and Newark Airport in New Jersey showed more of the same.

“I was in Houston [Thursday] trying to go through TSA, the lines were four hours,” travel expert and CBS News editor Peter Greenberg told Yahoo Finance. “And guess what? The average absentee rate there is over 40% at Bush Intercontinental, at Hobby [Airport] across town, it was 55%.”

At some airports, 40% to 50% of the TSA workforce called out on certain days, driving what TSA’s top official, Ha Nguyen McNeill, described as the highest wait times in TSA history, exceeding four-and-a-half hours.

Efforts to end the 41-day shutdown of the Department of Homeland Security saw a bipartisan breakthrough in the Senate early Friday, followed by an angry rejection when the measure reached the House.

The continued gridlock led to renewed uncertainty about what compromise is even possible to end the weeks-long logjam.

House Speaker Mike Johnson summarily rejected that approach Friday afternoon and announced that the House will pass a different bill to fund the entire Department of Homeland Security until May 22.

But the Senate, now in recess for the weekend, won’t be able to consider any new bill until Monday.

On Thursday evening, President Trump announced plans to sign an executive order to “address this Emergency Situation” and pay TSA agents without congressional approval. But it is unclear what legal authority that move would rely on. However, Johnson expressed confidence that the White House could move quickly, saying “that machinery is in process right now.”

Read more: Flight chaos grows as TSA lines stretch for hours. What to know about trip cancellation insurance.

For the airlines, missed flights and reduced capacity will hit the bottom line, and this doesn’t include the effect of higher fuel prices stemming from the US-Israel war against Iran.

The CEOs of American Airlines (AAL), Delta (DAL), United (UAL), Southwest (LUV), JetBlue (JBLU), Alaska Air (ALK), and several cargo carriers, including UPS (UPS) and FedEx (FDX), signed a joint open letter to Congress demanding an immediate end to the shutdown.

The CEOs, already smarting from last fall’s funding impasse that left TSA workers and air traffic controllers without pay, did not hold back.

“Once again, air travel is the political football amid another government shutdown,” the executives wrote via Airlines for America, an industry trade group. “TSA officers just received $0 paychecks. That is simply unacceptable. It’s difficult, if not impossible, to put food on the table, put gas in the car and pay rent when you are not getting paid.”

The industry expects a record 171 million passengers this spring, with the FIFA World Cup 2026 and America’s 250th birthday celebrations adding even more pressure on an already strained system this summer.

The joint letter warned that “too many travelers are having to wait in extraordinarily long — and painfully slow — lines at checkpoints,” leading to airlines holding flights and scrambling to rebook passengers, costs that compound daily.

Delta, the world’s largest airline by market capitalization, went further with its criticism.

Delta CEO Ed Bastian said in an interview with CNBC that he was “outraged” that security agents continue to work without pay, calling it “inexcusable” and accusing Washington of using frontline workers as “political chips.”

And the pain from snarled TSA lines and missed flights doesn’t include broader economic headwinds battering the industry.

Surging fuel prices tied to the ongoing US-Israel conflict with Iran are already squeezing margins.

Delta’s Bastian noted that the war in Iran adds additional layers of uncertainty that make planning for the busy spring and summer seasons extraordinarily difficult, with the hit from higher fuel costs touching $400 million alone in March.

At the center of the chaos are the TSA officers themselves — essential workers who are legally required to show up but are doing so with their compensation delayed.

TSA employees are dealing with eviction notices, vehicle repossessions, and even selling blood plasma for food money. Some officers have reported being unable to afford co-payments for cancer treatments or medical visits for sick children.

TSA’s McNeill, testifying before the House Homeland Security Committee on Tuesday, warned that the agency may be forced to close smaller airports entirely if staffing continues to deteriorate. McNeill also warned of travel woes that will continue beyond the shutdown, with an onboarding process for new hires that includes four to six months of training.

That’s because most TSA workers are in a dire predicament, and they need to work now.

“You have another situation where the average salary of a TSA agent is about $35,000 a year. That’s hand-to-mouth time, and they just literally have to go out and get second jobs. They can’t afford to be out of work,” Greenberg said.

Greenberg thinks the sheer pain felt by airlines, and even by D.C. politicians who are having problems traveling, means a solution could be coming soon.

“When you talk about long-term damage to the airline industry, historically, you’re really talking about self-inflicting wounds. They’re their own worst enemies, whether it’s government or the airlines themselves,” he said. “My guess is that this is going to get resolved relatively soon because of the economic impact.”

Whether it gets solved sooner rather than later, travelers like Mike Mayer believe Washington is the root of the problem.

“It’s the current political system, executive branch and legislative branch together, not working together to get the things that are important for the people,” he said.

“A lot of blame to go around.”

Pras Subramanian is Lead Auto Reporter for Yahoo Finance. You can follow him on X and on Instagram.

Click here for the latest technology news that will impact the stock market

Read the latest financial and business news from Yahoo Finance