The justices blocked a ruling that would have prevented the Pentagon from taking into account whether service members with religious objections were vaccinated.
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Navy service members prepared doses of Pfizer’s Covid-19 vaccine in Jacksonville, Fla., last year.
WASHINGTON — The Supreme Court on Friday restored the Navy’s ability to consider the vaccination status of 35 of its service members in decisions about where they should be assigned or deployed.
The court’s brief, unsigned order gave no reasons, which is typical when the justices act on emergency applications. The court’s three most conservative members — Justices Clarence Thomas, Samuel A. Alito Jr. and Neil M. Gorsuch — dissented.
In a concurring opinion, Justice Brett M. Kavanaugh said courts should not second-guess military officials.
“The Navy has an extraordinarily compelling interest in maintaining strategic and operational control over the assignment and deployment of all Special Warfare personnel — including control over decisions about military readiness,” he wrote.
Justice Kavanaugh added that he saw “no basis in this case for employing the judicial power in a manner that military commanders believe would impair the military of the United States as it defends the American people.”
In dissent, Justice Alito, joined by Justice Gorsuch, said the court did “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.”
“These individuals,” he added, “appear to have been treated shabbily by the Navy, and the court brushes all that aside.”
“The court’s order,” he continued, “essentially gives the Navy carte blanche to warehouse respondents for the duration of the appellate process, which may take years. There is no justification for this unexplained and potentially career-ending disposition.”
Justice Thomas noted his dissent but did not join Justice Alito’s opinion and provided no reasons of his own.
Judge Reed O’Connor, of the Federal District Court in Fort Worth, had issued a preliminary injunction barring the Navy from taking any punitive action against its personnel, including 26 SEALs, while their lawsuit moved forward. Judge O’Connor said the plaintiffs had religious objections to the coronavirus vaccine that the Navy had to respect.
After a unanimous three-judge panel of the U.S. Court of Appeals for the Fifth Circuit, in New Orleans, refused to block that ruling, the Biden administration filed an emergency application in the Supreme Court.
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The administration requested only partial relief, saying it did not seek to block the part of the injunction protecting the plaintiffs from discharge or discipline. Instead, Elizabeth B. Prelogar, the solicitor general, asked the justices to maintain “the Navy’s authority to decide which service members should be deployed to execute some of the military’s most sensitive and dangerous missions.”
Ms. Prelogar wrote that the injunction had already forced the Navy, against its military judgment, to send one of the plaintiffs to Hawaii for submarine duty. In general, she wrote, “Navy personnel routinely operate for extended periods of time in confined spaces that are ripe breeding grounds for respiratory illnesses, where mitigation measures such as distancing are impractical or impossible.”
She noted that the military had long required vaccinations, starting in 1777, when George Washington ordered the inoculation of the Continental Army against smallpox. As of early 2021, she wrote, nine vaccines were required for all service members.
In August, the Defense Department said it would add the coronavirus vaccine to the list. By the end of the year, more than 99 percent of active-duty Navy service members had been fully vaccinated.
But the 35 service members, all assigned to the Naval Special Warfare Command, refused, saying that their religious faith forbade them from being vaccinated against Covid-19. They had four kinds of objections, Judge O’Connor wrote: “opposition to abortion and the use of aborted fetal cell lines in development of the vaccine,” “belief that modifying one’s body is an affront to the Creator,” “direct, divine instruction not to receive the vaccine” and “opposition to injecting trace amounts of animal cells into one’s body.”
They asked for religious exemptions from the vaccination requirement, saying their requests had been or inevitably would be denied. They then sued, seeking to represent a class of thousands of Navy service members.
In his ruling, Judge O’Connor sided with the plaintiffs. “Our nation asks the men and women in our military to serve, suffer and sacrifice,” he wrote. “But we do not ask them to lay aside their citizenry and give up the very rights they have sworn to protect.”
The Supreme Court has historically been wary of second-guessing military judgments. Ms. Prelogar urged the justices to exercise similar caution in the new case, saying Judge O’Connor had effectively inserted himself into the Navy’s chain of command in a “severe and unprecedented intrusion into the operation of our nation’s armed forces.”
The Biden administration has had mixed success in defending its responses to the pandemic in the Supreme Court. In January, the justices blocked the administration from enforcing a vaccine-or-testing mandate for large employers, but they allowed a more limited mandate requiring health care workers at facilities receiving federal money to be vaccinated.
In his dissent on Friday, Justice Alito suggested that he would have approved of a narrower ruling, one limited “to the selection of the Special Warfare service members who are sent on missions where there is a special need to minimize the risk that the illness of a member due to Covid-19 might jeopardize the success of the mission or the safety of the team members.”
The majority’s broader ruling, he wrote, could have harsh consequences for the plaintiffs.
“It appears that the court’s order allows the Navy to use respondents’ unvaccinated status as a reason for directing them to perform whatever duties or functions the Navy wants, including sitting alone in a room pushing paper or reading manuals for the duration of the appellate process,” he wrote.
Justice Alito concluded his dissent by noting that the Supreme Court had ruled on Thursday for John Henry Ramirez, a death row inmate who had argued that he had a right to pray with and be touched by his pastor in the execution chamber.
“The contrast between our decision in Ramirez yesterday and the court’s treatment of respondents today is striking,” Justice Alito wrote. “We properly went to some lengths to protect Ramirez’s rights because that is what the law demands. We should do no less for respondents.”