United says about 97% of employees met vaccine deadline; Meanwhile, AA and Southwest pilots warn of travel chaos

United Airlines said Tuesday that less than 3% of its 67,000 U.S.-based employees applied for a religious or medical exemption to the airline's vaccine mandate, and that of the remaining, more than 99% had complied with the airlines vaccine mandate.

That left 593 employees who had failed to get vaccinated and upload their documentation, or apply for an exemption, by the Sept. 27 deadline, a senior executive said during a background briefing. Those employees will be fired over the coming days and weeks.

The airline said it expects no operational disruption from the termination of the non-compliant employees.

Employees who submitted for a medical or religious exemption would be placed on an unpaid leave, but the deadline for that has been extended due to pending litigation, CEO Scott Kirby said in a memo to employees viewed by TPG.

"We want to start by thanking the tens of thousands of employees who got their shot," Kirby and airline president Brett Hart wrote in the memo. "We know for some, that decision was a reluctant one. But there's no doubt in our minds that some of you will have avoided a future hospital stay — or even death — because you got vaccinated."

United's news came as pilots unions at American Airlines and Southwest Airlines warned that an exodus of pilots could occur if the federal vaccine mandate is implemented at airlines, potentially causing mayhem during the holiday travel period.

More: United doubles down on vaccine requirement with stringent policy for religious exemptions

About 30% of American Airlines pilots are unvaccinated, the pilots' union, the Allied Pilots Association, said, citing medical reasons and reluctance.

"We are also concerned that the Executive Order's anticipated 60-day implementation period for mandatory vaccinations could result in labor shortages and create serious operational problems for American Airlines and its peers," APA president Captain Eric Ferguson wrote in a letter to the Department of Transportation and the White House. "Airlines generate a substantial portion of their annual revenue during the holiday period, with a great many travelers depending on us to get them to their destinations. Our nation's airlines, and the traveling public, cannot afford significant service disruptions due to labor shortages."

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On Monday, a representative for the union representing American Airlines maintenance workers in Tulsa and Southwest Texas, Dale Danker, posted a video to YouTube protesting potential mandates and advocating for employees to refuse.

Both American and Southwest declined to comment.

The developments come as U.S. airlines have taken different tacks on encouraging their employees to get vaccinated, though United has been the most aggressive.

Delta Air Lines last month took a different approach to mandates, saying it would add a $200 monthly surcharge to unvaccinated employees' health insurance, citing the high cost burden of unvaccinated employees who end up hospitalized. If the Biden administration's executive order moves forward, the airline would likely also have to mandate vaccination or weekly testing.

The airline said that as of Sept. 23, 82% of its employees were fully vaccinated, up from 75% a month prior. A spokesperson for the airline said Tuesday that the rate was continuing to increase.