Southwest Airlines canceled nearly 5,000 flights Wednesday and Thursday of this week while trying to recover from an internal meltdown fueled by a winter storm as regulatory scrutiny grew.

Meanwhile, Southwest’s troubles may have been foreshadowed in a Dec. 21 internal company memo that highlighted a worker shortage in Denver, where Southwest has significant operations and which was pounded by the storm.

Southwest accounted for about 90 percent of Wednesday’s flight cancellations by U.S. airlines and about 99 percent of Thursday’s grounded flights. Other carriers appear to have recovered from the storm, posting typical numbers of cancellations, according to data from the tracking service FlightAware.

But at Southwest, more than 60 percent of Wednesday’s scheduled flights were scrubbed, along with a similar proportion of flights that had been scheduled for Thursday. Southwest’s 2,508 cancellations Wednesday were affecting air travel across the country with Chicago Midway International, Dallas Love Field and Baltimore-Washington International Marshall Airport seeing more than 30 percent of outbound flights canceled.

The disruptions echo last year’s turbulent Christmas and New Year’s holiday period, during which a combination of bad weather and a wave of coronavirus cases prompted thousands of cancellations. But this time around, Southwest stands alone among major airlines, prompting an inquiry by the Department of Transportation and the chair of the Senate Commerce Committee.

Company executives began sounding the alarm about staffing concerns in Denver on the day the storm was moving in. The carrier cited the storm’s effects in Denver and Chicago as factors in the service meltdown but also has said that the airline was staffed to handle the holiday travel period.

Southwest’s vice president for ground operations, Chris Johnson, declared a “state of operational emergency” because of an “unusually high number of absences” of Denver-based ramp employees, including sick calls and personal days for afternoon and evening shifts, according to the Dec. 21 memo, which was obtained by The Washington Post.

Ramp workers are crucial to keeping airline flight schedules running on time, helping planes park at gates and handling luggage. With Christmas approaching and a massive winter storm in the forecast, the company indicated that it needed all available employees.

“We have an obligation to our Customers and to our fellow Employees to safely and efficiently run our operation,” Johnson wrote.

The memo stated that employees “alleging illness” needed to provide a doctor’s note on the first day back to work that supported their reason for taking a sick day. Failure to do so could result in their being fired because of abuse of sick leave and for insubordination, Johnson wrote.

Johnson wrote that the company would deny requests for personal days during the state of emergency. Workers would be required to work overtime, if needed, under a mandatory overtime policy. Johnson said the operational emergency would remain in place until he lifted it.

Southwest officials have said the airline was not short-staffed before the storm pounded much of the country, citing the inability of internal logistics and scheduling systems to recover after widespread disruptions from the storm.

In an email, the company said operational emergencies are routine and contractually agreed-to by employees and union representatives. The company said the state of emergency was enacted only at Denver International Airport.

Robert Mann, who runs R.W. Mann & Company, an airline industry analysis and consulting firm, described the memo as draconian and said it may have had the opposite reaction that Southwest desired and could have prompted some workers to stay home, knowing they would be facing freezing temperatures.

“When it goes bad, it tends to go bad real quickly,” said Mann, a former airline executive.

Bob Jordan, Southwest’s chief executive, apologized to customers in a video message Tuesday, saying the carrier is aiming to recover by the end of the week. The airline has said it is struggling with outdated scheduling systems that have made it difficult to coordinate flight attendants. Jordan promised to upgrade those systems.

In the run-up to the busy winter travel season, Southwest had pointed to its strong hiring record in recent months. That recruitment drive appears to have been insufficient to stave off problems as the airline faces growing condemnation from its workers as the meltdown drags on

Airlines came under increased scrutiny this summer as cancellations rates climbed across the industry, with regulators looking for ways to hold carriers accountable for disruptions. Ahead of Labor Day, the Transportation Department posted a comparison of airline customer service policies, which officials said prompted some carriers to promise more help for stranded passengers.

Transportation Secretary Pete Buttigieg said his department would investigate Southwest’s handling of the cancellations. He called for airlines to temporarily cap fares on routes affected by Southwest cancellations to limit the financial burden faced by stranded or delayed Southwest passengers who are trying to book flights with other carriers. Buttigieg said most airlines had complied.

“What we’re seeing is something beyond what can be attributed to the weather,” he told ABC News.

Randy Barnes, president of TWU Local 555, which represents Southwest ground workers, said Wednesday that crews were working 16- to 18-hour days over the holidays, with some suffering frost bite as they worked in the cold.

“When you’re dealing with subzero temperatures, driving winds and ice storms, you can’t expect to schedule planes as if every day is a sunny day with moderate temperatures and a gentle breeze,” Barnes said.

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The Washington Post’s Keith L. Alexander contributed to this report.

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