The Supreme Court sided with the Biden administration Friday over Navy SEALs fighting the military’s COVID-19 vaccine mandate.

The court blocked a lower court’s ruling, which had prohibited the Pentagon from changing the military assignments of unvaccinated SEALs. Six of the nine justices on the court ruled that the Commander-in-Chief, not a judge, is ultimately in charge of the armed forces.

BREAKING: Siding with the Biden administration, the Supreme Court BLOCKS a lower-court ruling that had barred the Pentagon from considering the COVID vaccination status of Navy SEALs in making deployment decisions. Thomas, Alito, & Gorsuch dissent. https://t.co/w1dfsomMRZ

— SCOTUSblog (@SCOTUSblog) March 25, 2022

Texas U.S. District Court Judge Reed O’Connor ruled in January not only that the Navy must grant religious exemptions to the vaccine mandate to those who request them, but that commanders could not alter the assignments of troops based on their vaccination status. Friday, the Supreme Court put that order on hold, with dissents from Justices Gorsuch, Alito and Thomas. Alito wrote in a dissent separate from the others that the troops suing seemed to have been treated “shabbily” by the Navy, which denied their requests for religious accommodations to the vaccine mandate.

Defense Secretary Lloyd Austin said the lower court ruling “poses intolerable risks to safety and mission success,” and that the court was undermining the Navy’s authority. (RELATED: The Pentagon’s Vaccine Mandate Is Driving Yet Another Wedge Between Troops And Leadership)

The SEALs who were fighting the mandate now will likely face the prospect of limited deployment opportunities if they do not comply with the mandate. One commander of a guided missile destroyer has already had his ship’s deployment blocked due to his refusal to get vaccinated, as the Navy says he is a health threat to the other 320 sailors on board, according to NBC News.