The Supreme Court granted an emergency request from the Defense Department on Friday, temporarily freezing a lower-court ruling that required the Navy to deploy unvaccinated Navy SEALs.

The high court’s order temporarily blocks part of a January ruling by a federal judge in Texas that prevented the department from considering vaccination status in deployment decisions involving Navy special forces operators who sought a religious exemption.

The federal judge had sided with 26 members of the Navy SEALs and nine other special operations forces personnel who argued they are eligible for a religious exemption to the vaccine mandate because of the First Amendment. The Biden administration argued the lower court ruling usurped the Navy’s authority to deploy the servicemembers and execute missions.

The new order means the Navy can limit deployment and training of the group of SEALs and special operations forces personnel. U.S. District Judge Reed O’Connor also prohibited the Navy from enforcing the vaccine mandate against the 35 servicemembers involved in the suit, though the administration did not ask the Supreme Court to immediately lift that part of the order.

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Justice Brett Kavanaugh wrote in a concurring opinion that the district court,
while no doubt well-intentioned, in effect inserted itself into the Navy’s chain of command, overriding military commanders’ professional military judgments.”

“Under Article II of the Constitution, the president of the United States, not any federal judge, is the commander in chief of the armed forces,” Kavanaugh wrote. “In light of that bedrock constitutional principle, ‘courts traditionally have been reluctant to intrude upon the authority of the Executive in military and national security affairs.’”

Three conservative justices — Clarence Thomas, Samuel Alito and Neil Gorsuch — dissented. 

“By rubberstamping the government’s request for what it calls a ‘partial stay,’ the court does a great injustice to the 35 respondents – Navy Seals and others in the naval special warfare community – who have volunteered to undertake demanding and hazardous duties to defend our country,” Alito wrote in a dissent joined by Gorsuch. “These individuals appear to have been treated shabbily by the Navy, and the Court brushes all that aside. I would not do so, and I therefore dissent.”

The Biden administration told the Supreme Court that vaccine requirements are “the least restrictive means of furthering the Navy’s compelling interests in ensuring that members of the Special Warfare community are as physically prepared as possible to execute their demanding missions and in minimizing avoidable risks to mission success.”

Meanwhile, at least 98.5 percent of active and reserve members of the Navy have been vaccinated against Covid-19, USA Today reported.

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