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NEW YORK — Southwest Airlines canceled more than 1,000 flights Sunday, blaming massive nationwide disruptions on weather and air traffic control issues in Florida two days prior.

The flight-tracking website FlightAware.com shows that Southwest canceled 28% of its flights on Sunday while 600 more face delays. More than 800 Southwest flights were canceled Saturday and upwards of 1,100 flights were delayed, according to FlightAware.

For comparison, American Airlines has the second-most cancellations Sunday with 142, or 4%, as of 4:30 p.m. ET.

The colossal travel hiccup comes in the midst of a busy time for airlines — Monday is a federal holiday, meaning millions of American workers have a three-day weekend. More than 2.1 million people were screened at airport security checkpoints Friday, a volume that hasn’t been seen since early August, according to the Transportation Security Administration.

Videos and images posted to social media show Southwest customers waiting in long lines that snake through airports in Denver, New York, Missouri and Arizona. Travelers in Chicago, Houston and other major U.S. city reported similar turmoil.

“Hey @SouthwestAir … I’ll be missing my friends wedding because of you,” one person tweeted.

Southwest’s response

The Dallas-based airline tweeted Saturday that the problem stems from air traffic control issues and weather. In a more detailed statement issued Sunday, Southwest elaborated on how “weather challenges” and “unexpected air traffic control issues” in Florida on Friday created a ripple effect of nationwide delays and cancelations that spilled into the weekend.

“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 … With fewer frequencies between cities in our current schedule, recovering during operational challenges is more difficult and prolonged,” the statement said.

The Federal Aviation Administration also told ABC News that it has attributed a few flight cancellations and delays on Friday to severe weather, military training and limited staffing at the Jacksonville Air Route Traffic Control Center.

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

Southwest pointed affected customers to its self-service rebooking options on southwest.com. The airline said it is working to recover operations and thanks customers for their patience.

MORE: Southwest employees must be fully vaccinated by Dec. 8 to keep jobs, company announces

Anti-vaccine “work slowdown” could be catalyst for cancellations, analyst says

Henry H. Harteveldt, president and travel industry analyst at The Atmosphere Research Group, based in San Francisco, points to other causes for the cancellations.

First, he says Southwest has scheduled more flights than it can handle, a problem that started in June. He also noted that Southwest operates what’s known as a point-to-point route network, and when a delay occurs, it “cascades” along the remaining flight segments. That’s because, for example, a Southwest flight departing Fort Lauderdale, Florida, for the airline’s home base of Dallas may make multiple stops along the way.

But Harteveldt told The Associated Press the most troubling reason is the likelihood that some pilots who oppose Southwest’s decision to mandate COVID-19 vaccinations are participating in an illegal job action where they call in sick or are engaging in a “work slowdown.”

In a statement Saturday, the airline’s pilot union, Southwest Airlines Pilots Association, said that’s not the case.

“SWAPA is aware of operational difficulties affecting Southwest Airlines today due to a number of issues, but we can say with confidence that our pilots are not participating in any official or unofficial job actions,” it said.

Bad year for Southwest

Southwest has had a difficult year. The airline had the worst on-time performance and the greatest percentage of canceled flights of any of the nation’s four major airlines in June and July, according to flight-tracking service Cirium.

Passengers aren’t the only ones upset with Southwest: Unions for pilots, flight attendants and mechanics have all voiced complaints about the airline’s operations.

Southwest promised to address the problems by scheduling fewer flights in the fall.

But Harteveltd noted Southwest’s woes could linger and affect its fourth-quarter financial performance.

“All of this is happening as people are in the midst of booking their Thanksgiving and Christmas/New Year holiday travel,” he said. “It’s very possible that some people who might normally book on Southwest may see this news and choose to fly other airlines.”

The Associated Press and CNN Wire contributed to this report.

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