Thanksgiving holiday travel brought long security lines to Reagan National Airport this weekend as redesigned checkpoints faced their first major challenge during the busiest travel days of the pandemic era.

The wait early Sunday stretched to 45 minutes, forcing some passengers to run to their departure gates after getting through security. Airport and airline officials warned passengers Monday to allow extra time as parking garages, gates and airplanes record some of their most crowded conditions in nearly two years.

Cicely Simpson, 47, a lobbyist and leadership coach who splits her time between Nashville and Washington, said she grew worried when she saw the “sea of people” waiting to be screened Sunday morning.

“I saw that line. I thought, ‘Yeah, I’m going to have to find a new flight,’ ” she said. But Simpson, a frequent flier who has been making the journey between the two cities for two decades, is a member of the TSA PreCheck and CLEAR programs and said she was able to “breeze through.” But for those in the regular queue, “it was definitely the worst I’ve ever seen it for holiday travel,” she said.

The longer lines at National and warnings to be prepared for waits at airports across the country come as almost 6.5 million people passed through Transportation Security Administration gates nationwide between Friday and Sunday. Friday set a pandemic-era record for traveler volume, and the agency is expecting to screen 20 million people through next Sunday, a number approaching 2019 levels.

Despite the delays, officials reported no major problems during the first weekend of the holiday season.

Lisa Farbstein, a TSA spokeswoman, said there was no particular issue driving wait times at National, but people should be prepared to encounter lines as more people fly for the holidays. While some passengers were delayed, others said they quickly passed through security.

“Airports have rush hours like highways do,” Farbstein said.

There were other signs of high travel demand to start the holiday week. One parking garage at National was full for much of the weekend, said Christina Saull, a spokeswoman for the Metropolitan Washington Airports Authority. The garage had available spots again on Monday.

Saull said more people are choosing to drive during the coronavirus pandemic rather than take Metro or use ride-hailing services, adding that garages and the economy lot were close to full over Veterans Day weekend. The authority recommended that people heading to National or Dulles International Airport reserve a spot online if planning to park.

“Both airports are seeing a near-pre-pandemic level of holiday passenger traffic and the longer queues which come with an increase in passengers,” Saull said. “This is why we’re highly encouraging passengers to arrive at the airport at least two hours in advance for their holiday flight.”

Many travelers are encountering new checkpoints at National for the first time. The checkpoints opened this month as part of a $1 billion overhaul — the biggest at the airport since two terminals opened in 1997. Officials say the new system, a rare example of airport security designed with post-9/11 requirements in mind, will increase capacity and make it easier for passengers to get to their planes. But the weekend crowding left some travelers unsure.

“I would have expected a very different result given all the renovations,” Simpson said.

On Sunday, it appeared part of the problem was a bottleneck caused by a single security dog that was checking passengers. Past the dog, the line moved more quickly.

Saturday morning also had its share of traveler delays.

Frances Floresca recalled getting through security quickly before the pandemic — even during Christmas a few years ago — and that it took about 10 minutes. Heading to Atlanta on Saturday, she said, “I was expecting TSA to be smooth and quick, as usual.”

Instead, it took about 30 minutes.

“I am not a fan of the new TSA system,” she said.

Farbstein said travelers should expect to encounter crowds, noting that people are sharing checkpoints with some who haven’t flown since the start of the pandemic.

“A lot of parents are traveling with children for Thanksgiving week and they take a little longer at checkpoints,” she said. “And because people are new to travel or are rusty, they often have prohibited items in their carry-on bags, which also slows down the line.”

Jonathan Dean, a spokesman for Baltimore-Washington International Marshall Airport, said the weekend was smooth, with no significant waits at TSA or airline counters. The airport is expecting both Tuesday and Wednesday to set pandemic-era records, with 29,000 and 31,000 departing passengers, respectively.

“There is clearly a strong demand for travel,” he said.

Monday was the deadline for federal employees to be vaccinated against the coronavirus. The TSA said 93 percent of its workers were “in compliance with today’s deadline for the federal employee vaccine mandate and exemption requirements.”

The agency said it did not have data Monday on the breakdown of vaccinated employees and those seeking exemptions on medical or religious grounds. Employees who don’t comply could face termination, but the agency said the mandate would not affect holiday travel.

In Atlanta, police continued to search for a man who fled after a gun was discovered in his baggage Saturday at Hartsfield-Jackson Atlanta International Airport. The TSA said the man reached for the gun, accidentally firing it and causing a panic that led to flights being halted temporarily.

Andrew Gobeil, an airport spokesman, said operations were back to normal and officials were “expecting a very busy and enjoyable holiday week.”

During summer and early fall, some airlines experienced a wave of cancellations and delays, often the result of disruptions that began with bad weather cascading through their networks. Airlines have said they are prepared for the rush of holiday travelers, but some union leaders say domestic carriers remain short-staffed and vulnerable to problems.

Though there were no indications of widespread disruptions over the weekend, data from aviation tracking service FlightAware showed that about a third of flights on low-cost carriers Allegiant Air, Spirit Airlines and JetBlue Airways were delayed Sunday.

Hilarie Grey, a spokeswoman for Allegiant, said that there was no single cause for the delays but that high winds in Las Vegas, one of the airline’s major bases, posed problems for air traffic controllers, while bad weather in other cities also created challenges. Spirit and JetBlue did not respond to requests for comment.

Daron Taylor contributed to this report.