By Nathalie Voit

Southwest Airlines, one of the four major commercial airline carriers in the country, will comply with President Joe Biden’s executive order requiring employees to be vaccinated against Covid-19 amid a tumultuous weekend of cancellations, the airline announced on Oct. 12.

The federal executive order, signed into law on Sept. 9, requires all federal contractors to be vaccinated by Dec. 8. Like most major airlines, Southwest has contracts with the U.S. government and therefore considers itself subject to the White House rules.

Although the Executive Order has been in place for one month, a new decree issued Oct. 11 by Republican Gov. Greg Abbot of Texas blocking vaccine mandates by private employers left the Dallas-based company in a quandary over which orders to follow. The airline eventually noted its decision to comply with the federal rules Tuesday morning.

“We are reviewing all guidance issued on the vaccine and are aware of the recent Order by Governor Abbott. According to the President’s Executive Order, federal action supersedes any state mandate or law, and we would be expected to comply with the President’s Order to remain compliant as a federal contractor,” Southwest said in a statement to CBS 11 News Oct. 12.

The decision also affected other carriers with operations in the state, like American Airlines.

“We believe the federal vaccine mandate supersedes any conflicting state laws, and this does not change anything for American,” the Fort Worth-based airline said of the Texas ban.

Southwest CEO Gary Kelly, meanwhile, expressed his reservations against company-issued vaccine mandates but acknowledged the airline’s status as a federal contractor left the company in a bind.

“I’ve never been in favor of corporations imposing that kind of a mandate. I’m not in favor of that, never have been,” Kelly told CNBC on Oct. 12.

“But the executive order from President Biden mandates that all federal employees and then all federal contractors, which covers all major airlines, have to have a vaccine mandate in place by Dec. 8. So we’re working through that,” he said.

Kelly noted the company’s efforts to incentivize employees to get the Covid-19 shots by offering the equivalent of two days’ pay.

“The objective here is to improve health and safety, not for people to lose their jobs,” Kelly told CNBC.

The CEO’s comments came amid a prolonged weekend of mass cancellations that saw over 2,000 flights from Southwest grounded, according to the Wall Street Journal.

Many speculated the cancellations were due to walkouts from the vaccine mandates due to the timing. However, company representatives and the Federal Aviation Administration (FAA) blamed severe weather and air-traffic control issues in Florida for the delays.

“To be clear: None of the information from Southwest, its pilots union, or the FAA indicates that this weekend’s cancellations were related to vaccine mandates,” the FAA tweeted Oct. 11.

“We have some very strong views on that topic [Kelly said of the company’s 56,500 employees], but that’s not what was at issue with Southwest over the weekend,” he told CNBC.