Even as the Covid Omicron variant surge begins to shut US campuses, dozens of institutions have quickly reversed mandatory vaccine policies after a federal judge blocked a Biden administration requirement for them.

The institutions, largely in politically conservative southern and western parts of the US, suggested in some cases that the court ruling meant that they no longer were allowed to impose vaccination requirements.

The ruling by Stan Baker, a Trump-appointed federal court judge based in Georgia, does not itself outlaw vaccination mandates. But the judge’s rejection of the Biden policy leaves many institutions subject to the orders of their state government leaders, who have embraced and amplified Trump-era hostilities towards requirements for face masks and vaccines.

The likelihood of renewed campus closures was made clear by Cornell University, which shut its main campus in central New York state and shifted final exams online after tallying more than 900 new Covid cases in a week. Cornell has been requiring on-campus vaccination all semester, and as a private institution it is not affected by the Biden mandate or Judge Baker’s order against it.

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“We need to do what we can to limit further spread, even though we are just a few days away from the end of the semester,” Cornell’s president, Martha Pollack, to her Ivy League campus community.

Other institutions forced in recent days by Covid spikes to resume online instruction include Middlebury College and DePaul University – both of which also are private and have maintained on-campus vaccine requirements.

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In one announcement typical of the public campuses halting their vaccine mandates, Northern Arizona University said the court order “for the time being prohibits enforcement of the vaccination requirements for federal contractors”. The University of Wisconsin-Madison, ending its requirement, said the judge’s decision and other unspecified legal processes “may impact our campus’ ability to require the vaccine”.

The leading US higher education association countered such interpretations, making clear that the federal court ruling – upholding a claim brought by the University System of Georgia and several state government allies – only lifts the federal mandate.

“It’s important to note,” the 1,700-member American Council on Education said, “that these decisions don’t bar institutions in states that don’t prohibit vaccine requirements from moving forward with their policies.”

The ACE argued during the initial outbreak last year that the pandemic was so severe that it required a federal bailout of US higher education, and it succeeded in convincing Congress to provide nearly $70 billion (£50 billion) in emergency assistance to shuttered campuses. Now, with the US death toll from Covid hitting 800,000 and the Omicron variant pushing it higher, some of those same beneficiaries – having collected in federal recovery aid – are among the institutions refusing to require the protection of masks and vaccines.

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The University System of Georgia received more than $120 million in federal Covid relief aid. In bringing the lawsuit that prompted Judge Baker’s decision, it argued that public universities would “suffer significant harm” from a federal vaccine mandate. It was joined in the case by its own state government and by those of Alabama, Idaho, Kansas, South Carolina, Utah and West Virginia.

ACE’s general counsel, Peter McDonough, said campus reversals of vaccination mandates ultimately reflected political realities more than legal interpretations. For many campus leaders in particular states, he said in an interview, “you’re caught between a rock and a hard place”.

paul.basken@timeshighereducation.com