Commanders want to ensure they are following the rules, said Brig. Gen. Darrin Cox, surgeon general at Army Forces Command.

As deadlines loom for military and defense civilians to get mandated COVID-19 vaccines, senior leaders must now wrestle with the fate of those who flatly refuse the shots or are seeking exemptions, and how to make sure they are treated fairly and equally, the AP reports.

The vast majority of the active duty force has received at least one shot, but tens of thousands have not. For some it may be a career-ending decision. Others could face transfers, travel restrictions, limits on deployments and requirements to repay bonuses.

Exemption decisions for medical, religious and administrative reasons will be made by unit commanders around the world, on what the Pentagon says will be a “case-by-case” basis. That raises a vexing issue for military leaders who are pushing a vaccine mandate seen as critical to maintaining a healthy force, but want to avoid a haphazard, inconsistent approach with those who refuse.

Brig. Gen. Darrin Cox, surgeon general at Army Forces Command, said commanders want to ensure they are following the rules.

“Because of some of the sensitivities of this particular vaccine, I think that we just wanted to ensure that we were consistent and equitable” in meting out a punishment that would be “a repercussion of continuing to refuse a valid order.”

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