The Air Force has the military's first vaccine mandate deadline, Nov. 2. Some 12,000 Air Force personnel have said they won't get a shot, which means they'll face consequences.

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MARY LOUISE KELLY, HOST:

Today is the deadline for active-duty members of the Air Force and Space Force to be fully vaccinated against the coronavirus. They are the first up for the U.S. military branches. The Navy, Marines and Army deadlines are coming soon. Colorado Public Radio's Dan Boyce reports on what happens to troops who refuse the shots.

DAN BOYCE, BYLINE: The Pentagon says 97% of all active-duty personnel have had at least one shot. That's true for the Air and Space Forces as well. But an estimated 10,000 airmen and guardians remain unvaccinated. Some have qualified for exemptions. Failure to get vaccinated is against military law, and service members could face court-martial for it. But actually going that far is a bad idea, says Rachel VanLandingham, a law professor and president of the National Institute of Military Justice.

RACHEL VANLANDINGHAM: If they don't want to take the vaccination, fine. Then they're no longer - will be in the military. But they don't deserve the scarlet letter of a federal conviction that's going to follow them the rest of their lives for this.

BOYCE: Defense Secretary Lloyd Austin is not calling for stern discipline. At a press conference yesterday, Pentagon spokesman John Kirby said Austin is going to trust local commanders to use a range of enforcement tools with unvaccinated troops.

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JOHN KIRBY: I mean, I think the secretary's been very clear with the leaders of the military departments that he wants them to execute the mandate with a sense of compassion and understanding.

BOYCE: Still, Kirby says those commanders will ultimately do what they need to do for the readiness of their units. The Air Force has already dismissed nearly 40 trainees for refusing to be vaccinated. Meanwhile, the Navy says 99% of sailors have had at least one shot, the Marines are at 93% and the Army's last at 90%. Rachel VanLandingham says there's never been a mass refusal of a military vaccine requirement quite like this, a vaccine so highly politicized with such strongly held beliefs against it.

VANLANDINGHAM: There's a lot of misinformation, I think a lot of wrongly held beliefs, but that doesn't change their genuineness, their genuine conviction.

BOYCE: Because the vaccines are so politicized, she says this particular situation deserves a unique approach and one consistent across all military branches. The vaccination deadline for active-duty Navy and Marines is November 28. For the Army, it's December 15.

For NPR News, I'm Dan Boyce in Colorado Springs. Transcript provided by NPR, Copyright NPR.