Southwest Airlines made headlines over the weekend for a large number of cancellations of flights. The airline blamed weather and air traffic control staff shortages. There is speculation that the approaching deadline for airline personnel to get vaccinated against COVID-19 plays a role in the chaos. It looks like other airlines and even Amtrak may join in protesting the mandates.

There were 800 flights on Saturday and 1,000 flights on Sunday that were canceled by Southwest Airlines. The number of flights on Sunday amounted to about 30% of its flights. Customers found themselves stranded in airports and scrambling to make other travel arrangements. Airline pilots have warned that vaccine mandates may cause protests that disrupt air travel as we head into the busy holiday season. Biden signed an executive order mandating that most government employees and government contractors get COVID-19 vaccinations. Airlines are considered government contractors and receive contracts worth millions of dollars.

Airline employees usually participate in walk-outs instead of going on strike. Under the Railway Labor Act, in order to go on strike, airlines and its employees must go through a mediation process that is lengthy and designed to force a resolution between parties. If a resolution cannot be reached, the president can weigh in and order a cooling-off period. Employees are required to continue to work during that period. Congress can force both sides to accept a settlement, or may extend the cooling-off period indefinitely. So, in the case of airline pilots, for example, it isn’t as simple as just declaring a strike. Southwest Airlines’ pilot union is denying the cancellations were their fault.

On October 5 the union filed a temporary restraining order to stop Southwest from complying with the federal vaccination mandate. The union (SWAPA) released a statement. It blames poor planning as the cause of the cancellations.

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.

Alan Kasher, Southwest’s executive vice president of daily operations, said the airline didn’t anticipate the size of the disruptions.

“And as we’ve seen before, an unexpected number of delays ultimately leads to a staffing shortage, and at times, mandatory overtime because of the longer operating day. Although we’ve made schedule adjustments leading into the fall, our route system has not fully recovered—that will take time,” he wrote on the company’s intranet.

Airline sources: mass “sickout” @FAANews center in Jacksonville – caused ripple effect and 1000+ flight cancellations mostly effecting @SouthwestAir – report “sickout” protesting #VaccineMandate

— Leland Vittert (@LelandVittert) October 10, 2021

Ted Cruz tweeted about the havoc and blamed Biden.

Joe Biden’s illegal vaccine mandate at work!

Suddenly, we’re short on pilots & air traffic controllers.#ThanksJoe https://t.co/wviOzLt7Iv

— Ted Cruz (@tedcruz) October 10, 2021

Other airlines will also likely experience the same disruptions. The pilot union representing American Airlines is issuing a warning that staffing shortages may be coming during the holiday travel season. It is hoping the union members are allowed to request exemptions from the vaccine due to medical reasons. The deadline to show proof of vaccination is Nov. 24, the day before Thanksgiving.

The Allied Pilots Association requested that American Airlines find “alternate means of compliance with the Executive Order be made available for professional pilots” so as not to prompt mass firings and unpaid leave following President Joe Biden’s September announcement mandating large employers to require vaccinations or weekly testing.

“Some of APA’s members are unable to undergo vaccination for documented medical reasons, while others are reluctant to get vaccinated based upon concerns about the potential for career-ending side effects,” read the Sept. 24 letter.

“All of those members are still able to perform their duties as professional pilots,” the letter continued. “To force those pilots out of their positions, rather than offering viable alternatives will have adverse consequences upon their families and the airline industry as a whole.”

Most airlines have agreed to comply with the federal mandate. United Airlines was the first to report a successful turnaround of employee participation in getting vaccinated in order to keep their jobs. Delta went another route. Its CEO is uncertain about the federal mandate and instead implemented a $200 per month surcharge for unvaccinated staff. That policy put the compliance rate at 85% with an expected 90% rate by the end of the month.

“What we’re looking for is to ensure that there’s a pilot in the cockpit,” said Dennis Tajer, the spokesman for Allied Pilots Association. “If you suddenly one day have 4,000-plus pilots that are not able to fly, that’s a big deal. That’s worse than this past summer.”

But the largest pilots association and most major carriers — United Airlines, American Airlines, Southwest Airlines, JetBlue, Alaska Airlines and Hawaiian Airlines — confirm they will follow President Biden’s executive order requiring workers to get the shots.

For airline CEOs, it boils down to either comply with the mandate or lose federal contracts worth millions of dollars.

On August 11 Amtrak announced that as of October 1, all new hires must be vaccinated against COVID-19. All employees have until November 1 to be fully vaccinated. If they are not fully vaccinated, they will be required to submit a negative test result each week. Yesterday Amtrak tweeted about “unexpected crew issues” that caused cancellations. Is the alleged vaccine mandate sick-out spreading to train transportation, too?

Trains 465 and 416 departing on 10/10 are canceled due to unforeseen crew issues. Alternate transportation will be provided.

— Amtrak Northeast (@AmtrakNECAlerts) October 10, 2021

Most companies are allowing exemptions from the vaccines for medical reasons or religious reasons. “Unexpected crew issues” can mean anything but the timing is suspicious, given the alleged walk-outs experienced by Southwest over the weekend. The companies are being warned, though, by their unions. Being caught unprepared as the busy holiday travel season approaches will cause big hits to their reputations. If they are going to follow through on firing employees who don’t comply, hiring pilots, for instance, will be difficult due to the shortage most airlines are experiencing now. In the meantime, it sounds as though air travelers are going to have to pack some extra patience this year to visit Grandma for Christmas.