Air traffic disruptions are leaving American travelers increasingly frustrated this weekend as the record-long government shutdown forces widespread flight cancellations and delays at major airports. 

More than 16,000 flights were delayed on Saturday with more than 1,300 departures canceled altogether, according to FlightAware. Sunday isn’t shaping up to be much better, with 1,100 flights cancelled as of 6am eastern time. The airline watchdog posted a “Misery Map,” showing the airports suffering the worst cancellations and delays, with Atlanta, New York, and Chicago at the top of the list.

In an appearance of CNN’s State of the Union Sunday morning, Transportation Secretary Sean Duffy predicted that things would get worse in the coming days. “It’s only going to get worse,” he said. “Two weeks before Thanksgiving, you’re going to see air travel be reduced to a trickle.”

A frequent traveler, Raymond Alvarez, told KFOX14 in El Paso that he had waited through a two-hour delay before boarding his flight in Denver. “I do kinda worry about everything that’s going on,” he said. “We’ve been two hours set back, honestly, right now it was kind of rough.”

Another traveler, who asked not to be identified, was more accepting of the situation. “It’s a necessity that I’m going, so it doesn’t matter if I have to wait however long,” she told the El Paso station. “But I do have trust in God and trust in our president that the right thing will be done.”

The CEO of Frontier Airlines, Barry Biffle, acknowledged in a posting on LinkedIn that he cannot guarantee that all tickets booked on his airline will be honored.

“If your flight is canceled, your chances of being stranded are high, so I would simply have a backup ticket on another airline,” he wrote. “I’m sorry this is happening. Just giving everyone practical travel advice.”

The Federal Aviation Administration on Friday ordered service reductions at 40 high-traffic airports to manage staffing shortages among air traffic controllers, who have been working without pay for nearly a month.

The controllers have been calling out of work in increasing numbers amid the financial strain of the shutdown.

The mandated reductions began with a 4 percent cut in flights over this weekend and are scheduled to increase, reaching up to 10 percent by November 14, just a week before the start of the peak Thanksgiving travel period. Major hubs, including Newark Liberty International, John F. Kennedy International, and Chicago O’Hare International Airport, have experienced significant operational challenges. 

According to the FAA, departures to Newark were delayed by more than four hours due to staffing, while flights to JFK faced delays of nearly three hours. A ground stop was temporarily issued at Chicago O’Hare, grounding all departures from the airport.

But even an end to the  shutdown won’t bring an immediate resolution. Mr. Duffy said it will take time for all air traffic controllers to return to work, prolonging the impact on air travel.

And there is no guarantee that the currently scheduled reductions will be the last. “It is possible the Department of Transportation may ask airlines to cancel more than 10 percent of their flights if controllers keep calling out in higher numbers,” Mr. Duffy said.

To help ease congestion, the FAA has asked private jet operators to avoid the 40 affected airports and Mr. Duffy said private jet companies have been cooperative.

International flights remain unaffected by the cuts to avoid violating international agreements, Mr. Duffy said. “We have international agreements that we abide by, and because of those international agreements, I’m not going to impact those international flights.”

“If I do,” the secretary explained, “what will happen is we have other countries that are waiting to have a breach of those contracts from the U.S. so they can cut down American flights, and then that would have a very long lasting impact on our ability to send travelers from the U.S. to those partners.”

American Airlines blamed the whole mess on Congress. “Due to the prolonged government shutdown and nationwide air traffic control staffing shortages, we, like most airlines, are experiencing additional and widespread delays and cancellations across the country today despite the advanced cancellations that the FAA required us to make,” the airline said in a statement.

“We, again, urge leaders in Washington, D.C., to reach an immediate resolution to end the shutdown,” the airline said.