Southwest Airlines canceled hundreds of flights over the weekend, blaming the woes on air traffic control issues and weather.

The airline canceled more than 1,000 flights, or 28% of its schedule, as of 5 p.m. ET Sunday, according to flight tracker FlightAware. That was the highest rate by far of the major U.S. airlines. Next in line were Allegiant and Spirit, which had respectively canceled 5% and 4% of their flights on Sunday, according to the flight tracker. American Airlines canceled 2% of its flights.

Southwest Airlines said in an emailed statement that it had experienced weather challenges in its Florida airports at the beginning of the weekend, which were compounded by unexpected air traffic control issues in the same region. Those issues triggered delays and prompted significant cancellations for the airlines beginning Friday evening.

“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," said Southwest Airlines. “With fewer frequencies between cities in our current schedule, recovering during operational challenges is more difficult and prolonged."

The company said that it's allowing customers to explore self-service rebooking options on Southwest.com, where they can get updates on the status of their travel.

However, 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 says 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.

Harteveldt 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.”

By ANNE D'INNOCENZIO

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