The departure of veteran pilots, many with experience in Kosovo and the Gulf War, is creating huge holes in some military air units. CBS News spoke with over 100 pilots concerned about the vaccine.
"We're leaving the service of our country over fear of a shot," said retired Major Gary Blied of the U.S. Air Force Reserve. "And it just doesn't seem fair."
All military personnel are required to get the shots, despite doubts the vaccinations will protect troops from the deadly Anthrax virus in wartime. But it is fear of bad reactions to the vaccine itself that is leading many pilots to end long careers.
Randy Pzyk, a United Airlines pilot, quit flying for the Wisconsin Air National Guard rather than take the Anthrax shot.
"It was difficult," Pzyk recalled. "I cleaned out my locker, stripped my name off my mailbox and packed up and left."
Key units across the country stand to lose up to half of their pilots. At five bases combined, more than 100 reserve pilots quit this year. Major Ramona Savoie is one of them.
"The squadron is unable to do its peacetime and wartime mission," Savoie said. "And this directly impacts the nation's readiness."
Pentagon officials insist the vaccine is safe, pure and effective -- and say the vaccination program is going smoothly.
"Generally speaking, this is not a significant issue. It has not had any effect on readiness at this juncture," said Charles Cragin, Assistant Secretary of Defense for Reserve Affairs.
But military memos obtained by CBS News tell a different story. One squadron commander writes, "Due to the controversy regarding the shots, compliance has been very low." Another acknowledges, "We are losing a lot of experience."
Most experienced Guard and reserve pilots fly passenger jets as their main job. Pilots like Mike Angerole of Southwest Airlines are quitting the Air Guard rather than risk vaccine side effects that could endanger their passengers.
"Would you want your pilot to have any problem with remembering, and tremors, seizures," Angerole said. "And this is all stuff that's attributed to the vaccine."
So far, Pentagon officials are refusing pilot requests to make the shots voluntary. In a letter to the Army Times, Defense Secretary William Cohen writes, "Just as soldiers must wear helmets, commanders must know all their troops are vaccinated against anthrax."
"I'm more than willing to lay my life down for my nation. Is that not enough?" Angerole said.
Not for the Pentagon apparently, which says no matter how many pilots quit - the vaccinations will continue.
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