In the early days of the litigation against the Department of Defense’s COVID-19 vaccine mandate, courts were understandably hesitant to second-guess military judgments about mission accomplishment and readiness. But recent developments indicating that not all military commanders agree with punishing and discharging service members with sincere religious objections to the vaccine mandate might stretch the limits of judicial deference to military judgments.

First Liberty Institute filed one of the first lawsuits against the Department of Defense vaccine mandate in November 2021. In January 2022, a federal district court judge issued an injunction that prohibits the Navy from taking any adverse action against members of the Navy SEALs because of their sincere religious objections to the Department of Defense vaccine mandate. In early March, the Fifth Circuit rejected the Navy’s request that it stay the injunction. But on March 25, the Supreme Court, in a 6-3 decision, granted the Biden Administration’s emergency application for a partial stay that allows the Navy to consider vaccination status when making “deployment, assignment, and other operational decisions.”

In a concurrence, Justice Kavanaugh explained that he voted in favor of the Navy due to the “bedrock constitutional principle” that courts ought not interfere with executive authority over military and national security matters, and that judges should give broad deference to military commanders’ judgments.

U.S. Air Force Lieutenant Colonel Jonathan Dunn sued the Air Force because of its denial of his religious accommodation. After unfavorable rulings from a federal district court judge and the Ninth Circuit, Dunn filed his own emergency stay application at the U.S. Supreme Court. But in another 6-3 decision, the Court again ruled in favor of the Department of Defense, presumably due to the same rationale Justice Kavanaugh offered in the SEALs case.

Mandatory vaccinations have long been a contentious subject in America, so it comes as no surprise that the COVID-19 vaccine mandate is no different. Legal experts are fairly divided. Some commentators point to prior court decisions that addressed military orders and religious objections in support of Justice Kavanaugh’s position, while others argue that such religious objections are “farfetched” and lack sincerity. The military, they argue, should enjoy broad deference in deciding whether to make the vaccine mandatory, and how to handle those who object.

But new evidence suggests that the military judgments regarding COVID-19 vaccination to which courts defer are being overlooked by political leaders.

In March, three dozen Air Force members filed a new lawsuit challenging the denial of their religious accommodation requests to the COVID-19 vaccine mandate. Invoking Justice Kavanaugh’s concurrence, the Air Force’s attorney defended its actions saying, “The commanders on the front line are in the best position to evaluate the level of risk. We are going to have to rely on the commanders to make the decision.”

But many front-line commanders actually recommend approval of religious accommodations from the vaccine mandate. One Air Force officer testified that his religious accommodation request was reviewed by a six-person “religious review team,” who recommended approval, and his commander agreed.

A Navy chaplain disclosed that despite two levels of his command recommending approval of his religious accommodation request, “it was ultimately rejected ‘at the top.’”

Thus, it appears Pentagon officials are ignoring the recommendations and efforts of front-line commanders—those who they say are “in the best position to evaluate the level of risk”—to approve religious accommodation requests. It is also possible some commanders believe that accommodating religious objectors—who amount to a small fraction of the entire military—will not harm military missions, but they do not speak up because they fear retribution for straying from the official line.

These concerns prompted Members of Congress to seek answers from Secretary of Defense Austin about how the Pentagon handles religious accommodations and the COVID-19 vaccine mandate. For its part, the Department of Defense Inspector General quietly initiated an internal audit to determine whether the Pentagon is violating federal law and Department of Defense regulations in its handling of religious accommodation requests.

The U.S. military has successfully navigated the COVID-19 waters since the earliest days of the pandemic, and even before vaccines were available, service members were safely deployed around the globe to serve on successful missions. The loss of personnel who fail to comply with the vaccination mandate—many of whom are seasoned, experienced leaders—poses a far greater threat to mission accomplishment and readiness than does COVID-19 at this juncture. Front line military commanders know this. Perhaps the Pentagon knows, too. But it still refuses to relent in its effort to purge the military of any and all who, on the basis of conscience, refuse the vaccine.

While it is true that the military generally enjoys wide latitude and deference when it comes to judicial review of military judgments, the military should forfeit that latitude and deference when it abuses its authority and violates federal laws protecting religious freedom. If our nation and our military are to remain the greatest on earth, service members of faith must be treated with dignity, tolerance, and respect. Religious liberty is essential to national security.

Note from the Editor: The Federalist Society takes no positions on particular legal and public policy matters. Any expressions of opinion are those of the author. To join the debate, please email us at info@fedsoc.org.