Southwest Airlines tries to return to normal but some flight cancellations persist.

The airline and its pilots union denied that the cancellations were related to the company’s decision to require employees to be vaccinated against the coronavirus.

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Southwest Airlines tries to return to normal but some flight cancellations persist.

A Southwest Airlines plane at Hollywood Burbank Airport in California on Sunday.Credit…Robyn Beck/Agence France-Presse — Getty Images

Oct. 11, 2021, 1:47 p.m. ET

Southwest Airlines canceled several hundred flights on Monday as it worked to resolve the problems that led it to strike more than a quarter of its scheduled flights last weekend.

Over 1,800 Southwest flights were canceled on Saturday and Sunday, accounting for more than 28 percent of its flights over the weekend, according to FlightAware, a tracking service. By noon on Monday, Southwest had canceled about 10 percent of the flights scheduled for the day, just over 360 flights.

The cancellations wreaked havoc on travel plans for thousands of passengers, many of whom vented their frustrations on social media. At least some were trying to make it to the Boston Marathon, which was canceled last year and delayed by six months this year.

The airline and the union that represents its pilots, the Southwest Airlines Pilots Association, said the disruption was not caused by protests over the airline’s recently announced vaccination mandate, denying an idea that had gained traction online among conservatives and anti-vaccination activists. Conservative lawmakers pointed to Southwest’s cancellations as evidence that vaccine requirements could harm the economy.

“Joe Biden’s illegal vaccine mandate at work!” Senator Ted Cruz, Republican of Texas, said Sunday night on Twitter. “Suddenly, we’re short on pilots & air traffic controllers.” Senator Ron Johnson, Republican of Wisconsin, echoed those comments on Monday.

Southwest blamed the cancellations on several causes, including problems with the weather, air traffic control and inability to get flight crews and planes to where they were needed.

“We experienced weather challenges in our Florida airports at the beginning of the weekend, challenges that were compounded by unexpected air traffic control issues in the same region, triggering delays and prompting significant cancellations for us beginning Friday evening,” the airline said in a statement. “We’ve continued diligent work throughout the weekend to reset our operation with a focus on getting aircraft and crews repositioned to take care of our customers.”

The Federal Aviation Administration acknowledged that some flights were delayed or canceled on Friday because of severe weather, military training exercises and a brief staffing shortage at one air traffic control center, but it said the disruption only lasted a few hours.

“Some airlines continue to experience scheduling challenges due to aircraft and crews being out of place,” the agency said in a statement.

Casey Murray, the president of the Southwest pilots union, said pilots called in sick at a normal rate this weekend.

The widespread cancellations, he said, were instead caused by technological issues and problems with how pilots are reassigned and rerouted during disruptions, a process complicated by Southwest’s uniquely large, point-to-point network. In a typical day, about 10 percent of pilots are reassigned from the flights they were scheduled to operate. That figure was 71 percent on Saturday and 85 percent on Sunday, according to Mr. Murray.

“That is unsustainable,” he said. “The domino effect continues, and what we see, due to some internal failures, is it’s happening so many times that they just can’t move everyone.”

The union also said in a statement on Sunday that its members are barred by federal law from using a strike to resolve a labor dispute without exhausting other options first.

While the union, which says it does not oppose vaccination, denied that its members were calling in sick to protest the mandate, it did ask a judge on Friday to stop the airline from enacting the vaccine mandate and other policies. The request is part of a broader lawsuit that predates the mandate and centers on the union’s assertion that Southwest has taken a number of “unilateral actions” in violation of labor law.

Southwest isn’t alone in seeing pushback from employees over a vaccine mandate. Last week, hundreds of American Airlines workers and supporters protested its new mandate outside that airline’s Fort Worth, Texas, headquarters, according to The Dallas Morning News.

But many others have voiced support for such requirements. United Airlines, the first large U.S. airline to impose a mandate, has said that nearly all of its 67,000 employees had been vaccinated, with the exception of about 2,000 who had applied for religious or medical exemptions. United said it expects to have to fire fewer than 250 employees for failing to comply. The airline’s executives had expected some blowback but were surprised by the positive reaction, noting that it had received many more applicants for open flight attendant positions than it used to before the pandemic.

“I did not appreciate the intensity of support for a vaccine mandate that existed, because you hear that loud anti-vax voice a lot more than you hear the people that want it,” United’s chief executive, Scott Kirby, told The New York Times this month. “But there are more of them. And they’re just as intense.”

Delta Air Lines has not imposed a vaccination requirement, but it said it will charge unvaccinated employees $200 more a month for health insurance.

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