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A federal judge ruled on Tuesday that New York State health officials must allow employers to grant religious exemptions to a Covid-19 vaccine mandate for health care workers while a lawsuit challenging the mandate makes its way through the courts.

The judge’s order at least temporarily thwarts Gov. Kathy M. Hochul’s effort to require immediate vaccination for health care workers even if they have religious objections. And it offers a reprieve for thousands of unvaccinated doctors, nurses and support workers who would have been prevented from working beginning Tuesday if the judge had ruled for the state.

A lawyer for a group of health care workers who are suing the state over the mandate hailed the ruling.

“With this decision, the court rightly recognized that yesterday’s ‘front line heroes’ in dealing with Covid cannot suddenly be treated as disease-carrying villains and kicked to the curb by the command of a state health bureaucracy,” said Christopher Ferrara of the Thomas More Society.

Ms. Hochul, in a statement, indicated the state would appeal.

“My responsibility as governor is to protect the people of this state, and requiring health care workers to get vaccinated accomplishes that,” Ms. Hochul said. “I stand behind this mandate, and I will fight this decision in court to keep New Yorkers safe.”

Former Gov. Andrew M. Cuomo issued the state’s first vaccine mandate for health workers in mid-August; it permitted religious exemptions.

But when Ms. Hochul’s administration issued its own mandate later that month — to take effect this fall — it rescinded the exemptions. That prompted 17 health care workers to sue the state in federal court, on the ground that the mandate conflicted with their religious beliefs.

Between the two governors’ orders, thousands of health care workers across the state had applied for or received a religious exemption.

In his 27-page ruling, Judge David N. Hurd of the Northern District in Utica wrote that New York appeared to overreach by barring all religious accommodations in the mandate. He issued a preliminary injunction preventing the Department of Health from acting against any employer who grants religious exemptions, and wrote that the 17 health care workers were likely to succeed in their case.

“The Department of Health is barred from interfering in any way with the granting of religious exemptions from Covid-19 vaccination going forward, or with the operation of exemptions already granted,” Judge Hurd wrote.

What to Know About Covid-19 Booster Shots

The F.D.A. authorized booster shots for a select group of people who received their second doses of the Pfizer-BioNTech vaccine at least six months ago. That group includes: Pfizer recipients who are 65 or older or who live in long-term care facilities; adults who are at high risk of severe Covid-19 because of an underlying medical condition; health care workers and others whose jobs put them at risk. People with weakened immune systems are eligible for a third dose of either Pfizer or Moderna four weeks after the second shot.

Regulators have not authorized booster shots for recipients of the Moderna and Johnson & Johnson vaccines yet, but an F.D.A. panel is scheduled to meet to weigh booster shots for adult recipients of the Moderna and Johnson & Johnson vaccines.

The C.D.C. has said the conditions that qualify a person for a booster shot include: hypertension and heart disease; diabetes or obesity; cancer or blood disorders; weakened immune system; chronic lung, kidney or liver disease; dementia and certain disabilities. Pregnant women and current and former smokers are also eligible.

The F.D.A. authorized boosters for workers whose jobs put them at high risk of exposure to potentially infectious people. The C.D.C. says that group includes: emergency medical workers; education workers; food and agriculture workers; manufacturing workers; corrections workers; U.S. Postal Service workers; public transit workers; grocery store workers.

It is not recommended. For now, Pfizer vaccine recipients are advised to get a Pfizer booster shot, and Moderna and Johnson & Johnson recipients should wait until booster doses from those manufacturers are approved.

Yes. The C.D.C. says the Covid vaccine may be administered without regard to the timing of other vaccines, and many pharmacy sites are allowing people to schedule a flu shot at the same time as a booster dose.

The judge had earlier issued a temporary restraining order barring the state from enforcing the mandate against people with religious objections starting in mid-September; technically, Tuesday’s order extended that ruling. The restraining order effectively allowed many health workers who applied for religious exemptions in New York to continue working even after the mandate went into effect.

In the federal case, titled Dr. A et al v. Hochul, the 17 health care workers argued that they could not consent to be inoculated with vaccines “that were tested, developed or produced with fetal cell lines derived from procured abortions.”

Pope Francis has said that Catholics may get the Covid-19 vaccines; most of the health care workers suing in the case are Catholic. But Judge Hurd did not question whether the health care workers were correct in their religious objections. Instead, he focused on their broader constitutional right to have their religious beliefs considered, and when possible, accommodated.

In his ruling on Tuesday, Judge Hurd looked at how the mandates differed from one governor to the next. “This intentional change in language is the kind of ‘religious gerrymander’ that triggers heightened scrutiny,” the judge wrote.

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