A judge says New York must allow religious exemptions, for now, to its health care worker vaccine mandate.

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 Hochul’s administration issued its own mandate later that month — to take effect this fall — it rescinded the exemptions.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.

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.