• Southwest has cancelled more than 1,800 flights over the weekend so far.
• The Dallas-based airline blamed the disruptions on air traffic control issues, bad weather and staffing shortfalls.
• Other airlines that operate in the region reported far fewer cancellations.

Southwest Airlines canceled more than 1,800 flights this weekend, disrupting the travel plans of thousands of customers and stranding flight crews — the airline blamed the meltdown on a combination of bad weather, air traffic control issues and its own shortage of available staff.

"I know this is incredibly difficult for all of you, and our Customers are not happy," Alan Kasher executive vice president of daily flight operations told staff in a note on Sunday, which was seen by CNBC.

The airline said initial problems on bad weather and an "FAA-imposed air traffic management program" were to blame.

"Although we were staffed for the weekend, we could not anticipate the significant disruption that was created from unexpected ATC issues and bad weather across our Florida stations," said Kasher.

Other airlines canceled relatively few flights. Southwest did not comment on the disparity.

The Federal Aviation Administration said there were a "few hours" of flight delays on Friday afternoon because of severe weather and staffing issues at Jacksonville Air Route Traffic Control Center, which controls airspace in five parts of Alabama, Georgia, Florida, North Carolina and South Carolina.

"No FAA air traffic staffing shortages have been reported since Friday," the FAA said. "Some airlines continue to experience scheduling challenges due to aircraft and crews being out of place. Please contact the airlines for details about current flight schedules."

Southwest's major destinations of Denver, Baltimore, Dallas Love Field and Chicago Midway were among the hardest hit by the cancellations on Sunday.

Southwest apologized to travelers for long customer service waits. The airline said in a statement it expected to get close to normal operations by Sunday, but disruptions worsened.

Southwest's Kasher acknowledged to employees in his note Sunday that some crew members didn't have hotel rooms last night and said disruptions can quickly snowball as flight crews hit contractual and federal working limits.

"Right now, our [network operations center] Teams are working to protect our Crew network and prevent misconnects — both for our Crews and Customers — that would cause an even greater impact," he said. "And Teams are working to determine the best course of action to most quickly reset our network."

The Dallas-based airline canceled 1,019 flights on Sunday, 28% of its schedule, after canceling 808 flights on Saturday, according to flight-tracking site FlightAware. American Airlines, which operates a large hub in Miami, in comparison, canceled 66 mainline flights, or 2% of its operation on Saturday and Fort Lauderdale, Florida-based Spirit Airlines canceled 32 flights, 4% of its schedule.

Staffing shortages fueled hundreds of cancellations and delays at Southwest over the summer. The airline trimmed its schedule after the summer to avoid further disruptions. Other airlines also faced a shortage of workers after encouraging thousands to take leave or buyouts at the height of the pandemic, only for travel demand to return faster than expected this summer.

"Although we've made schedule adjustments leading into the fall, our route system has not fully recovered — that will take time," Kasher said. He said the airline has fewer frequencies between major airports to reroute or rebook travelers. Southwest doesn't have so-called interline agreements that large airlines like Delta and American have to book travelers on other carriers.

Southwest had 3,614 flights scheduled on Sunday, the most since April 2020 and down 8% from the same day in 2019, before the pandemic, according to aviation consulting firm Cirium.

The airline has struggled to hire new employees in the tight labor market. Incoming CEO Bob Jordan told CNBC last month that the carrier is prepared to cut flights over spring break season if it doesn't have enough staff to support the operation.

The disparity between Southwest's operation and other airlines fueled speculation on social media that employees were calling out sick, with some suggesting it was in protest of a Covid vaccine mandate. Southwest said that was not the cause of the mass flight cancellations.

"It's inaccurate," a Southwest spokeswoman said by email. "There's a lot of unfounded rumor and speculation circulating."

The Southwest Airlines Pilots Association, Southwest pilots' labor union said that "we can say with confidence that our Pilots are not participating in any official or unofficial job actions."

"Our Pilots will continue to overcome SWA management's poor planning, as well as any external operational challenges, and remain the most productive Pilots in the world," it said.

Earlier on Saturday, the union said that the company's announcement last week that it will join other airlines in complying with the Biden administration's requirement that federal contractors must mandate Covid vaccinations is contributing to distractions for aviators.

"Make no mistake about it – due to months of staffing issues and inefficient scheduling practices we have been operating at a higher than normal operational risk," the union's safety committee told members in a post on Saturday.

It said reports of fatigue, which require pilots not to fly, are triple historic norms.

"All of these challenges have led to an added distraction in the cockpit," it said. "This week's COVID-19 vaccine mandate announcement by the Company only exacerbates the situation."

On Friday, the labor union asked a federal court in Dallas to temporarily block the implementation of the vaccine mandate and other Covid-19 policies, arguing the company took unilateral decisions that require negotiations with the union.