Security lines stretched for hours on Monday at US airports where unpaid Transportation Safety Administration (TSA) screening agents refused to report for duty and ICE agents deployed by Donald Trump were reportedly seen in a dozen cities.

The president claimed over the weekend that immigration agents could help manage long lines, but in Atlanta, little immediate impact of their presence could be observed. Meanwhile, airport staff were getting creative trying to herd thousands of discontented passengers.

Lines at Hartsfield Jackson international airport had spilled out from the screening area, winding inside and out of the staging area, the baggage claim and at 9am were in a loop on the curb. People hoping to make mid-morning flights had been standing in line since before sunrise.

Screening agents from the TSA have gone unpaid while the Department of Homeland Security (DHS) remains partially shut down. The budget impasse in Washington DC stems from demands by Democratic lawmakers to hold immigration enforcement agents to account after the killings of Renee Good and Alex Pretti in Minneapolis, and practices of warrantless detention and militarized raids that have raised alarms.

TSA agents missed their second paycheck on Friday. Many are not showing up for work and hundreds have reportedly quit.

“Pay these people!” shouted Dr Paul Brown, president and dean of the Phillips School of Theology in Atlanta, an hour into his wait for screening before a flight to Indianapolis on Monday. “Help explain to me that the congresspeople – they’re getting paid on time regularly, no problem. But these people who work for $40,000 a year, you’re holding them up over some politics.”

Brown scoffed at the suggestion that ICE agents at airports would be helpful. “It doesn’t matter,” he said, citing the budget impasse as a consequence of their conduct in the field. “They’re part of the problem.”

Trump deployed ICE agents to assist with passenger screening in 11 cities with busy airports on Monday, according to CNN, including Atlanta, Chicago, Philadelphia, Houston, Phoenix, Cleveland, Ft Myers, New Orleans and the New York City area’s three big airports, JFK, Newark and LaGuardia, where a plane crashed into a truck this morning, killing two pilots.

The fatal crash has caused the airport to shut down and effects to ripple throughout the system.

“It’s total chaos,” said Tom Healey of Alpharetta, Georgia, trying to make a flight to Louisville from Atlanta. He had been in line for three hours by 8am; his flight was scheduled for about 9. “Look at what happened at LaGuardia,” he said. “My wife’s got to fly out of that place. She was supposed to fly out of LaGuardia today.”

Karan Ghura had been in line since 4am. At 9.30, he had already missed his flight to Phoenix and was standing in line – again – to make a different flight home to the Bay Area.

“The funny part is, when I put my flight details in, Clear tells you what time you should come. They told me to leave at 4. There’s no way I can come and leavethe place I was staying at 4 and catch my 6 with this kind of traffic.”

Clear service allowing passengers to bypass security lines was down. An agent in Atlanta attributed it to staffing shortages.

“Clear remains open and ready to serve our members for PreCheck passengers in the main terminal and all passengers in the international terminal,” said Kyle McLaughlin, executive vice-president of aviation at Clear. “Due to circumstances beyond our control, airport conditions are changing rapidly and may affect service in some of our locations.”

Screening times have varied greatly, depending on the airport and differences between the morning peak and midday travel. LaGuardia did not reopen after the crash until 2pm, and the closure affected connections across the country. In Houston, a joke that it might be faster to drive to Austin than fly there is being taken in earnest, given three-to-four-hour screening queues at the peak and a two-and-a-half hour drive.

But Chicago’s wait times appear negligible. And while three screening stations have been shut down in Philadelphia for days, the airport is reporting wait times under 15 minutes.

Meanwhile, dozens of ICE agents could be seen unmasked in Atlanta’s terminals. Trump claimed on Monday morning that agents are now able to “arrest illegals as they come into the country. That’s very fertile territory.” But, Trump, added, they were really there to help.

The Atlanta mayor, Andre Dickens, said: “According to federal officials, these personnel will be assigned to support operational needs directed by the Transportation Security Administration including line management and crowd control within the domestic terminals. Federal officials have indicated that this deployment is not intended to conduct immigration enforcement activities.”

Their presence met political condemnation from administration critics.

“Trump’s secret police are now stationed at airport checkpoints,” said NAACP national president Derrick Johnson. “They are inadequately trained, armed, and instructed to profile people based on race and accent. What could possibly go wrong? We’ve seen this movie before. Don’t forget that Trump’s cronies in Congress tanked a proposal to pay TSA agents. This is a deliberate decision, it’s not a bandaid for a lapse in funding.”

Tamika West, who was trying to fly home to Fort Lauderdale, Florida, on Monday, said she was buying a ticket for a new flight, unable to get through the lines quickly because her Clear membership was not going to help. A half-dozen ICE agents were standing behind her in a cluster, watching the crowds.

“So, how do they help?” she asked. “How are they helping when the line is wrapping around every bag carrier, baggage claim and all that. How are they helping? They’re not helping. They’re making it worse.”

Tina Deschler was flying home Monday afternoon from Atlanta to Milwaukee. It took her about an hour and forty minutes to clear screening, and welcomed the presence of ICE at the airport.

“It’s probably important that they’re here,” she said, noting their potential to improve airport security. “Because people are standing in these lines for two, three, four hours and it could get a little chaotic. Hopefully they could put the fires out.”

Donta Knight was flying to Kansas City at the same time, and was less confident in ICE’s ability to help.

“I don’t see the purpose of it,” he said. The answer is to pay the workers, he added. “So they will come to work and make this go easier and smoother for all of us.”

Amid the anxiety about ICE agents’ presence at the airports, video went viral of a struggle between a woman and two federal immigration agents at San Francisco international airport on Sunday. But local officials on Monday said the encounter did not stem from an arrest at the airport – and that the agents involved had been transporting the woman as well as a child on an outbound flight when the incident happened, the San Francisco Chronicle reported.

“We believe this is an isolated incident and have no reason to suspect broader enforcement action at” the airport, Doug Yakel, a facility spokesperson said in a statement reported by the Chronicle.