Updated at 1:50 p.m. ET

In a blow to the Trump administration, a federal court in Manhattan has knocked down a rule that would make it easier for doctors and other health care workers to refuse care for religious reasons.

U.S. District Judge Paul Engelmayer ruled Wednesday that the Department of Health and Human Services, which issued the regulation earlier this year, exceeded its authority and "acted arbitrarily and capriciously" in promoting it.

The department's violations of federal law, according to the judge's opinion, were "numerous, fundamental, and far-reaching" — and he vacated the rule entirely, just over two weeks before it was set to take effect on Nov. 22.

The Trump administration had asserted that the rule would give health care providers the freedom to opt out of providing care or services — such as abortions — that violate their conscience. Employers that did not comply with the rule could have had their federal funding withdrawn.

"This rule ensures that healthcare entities and professionals won't be bullied out of the health care field because they decline to participate in actions that violate their conscience, including the taking of human life," Roger Severino, director of HHS's Office for Civil Rights, argued in a written statement when the regulation was issued in early May.

The rule's critics, however, saw it as a means of allowing health care workers to circumvent rules against discrimination. And they quickly took the Trump administration to court — with more than two dozen states, cities and organizations such as Planned Parenthood filing lawsuits against Severino and Health and Human Services Secretary Alex Azar. Those suits were later consolidated into one case, which Engelmayer oversaw.

There's also another lawsuit against this rule, filed in the U.S. District Court for the Northern District of California. The plaintiffs in that consolidated case include the state of California, Santa Clara County and organizations such as Lambda Legal. It wasn't immediately clear what Wednesday's ruling means for the case in California.

As NPR has reported, this rule was part of a big push from the Office for Civil Rights to bolster "religious freedom" in health care. Severino, who is Catholic and formerly of the conservative Heritage Foundation, has argued that previous administrations did not fully enforce existing law that protected what supporters call health care workers' "conscience rights."

To remedy that, Severino created a Conscience and Religious Freedom Division in January 2018, and in May of this year, his office issued this rule.

The rule was designed to bolster the rights of providers to opt out of care, even without prior notice of their objections to their employer. It also expanded the type of workers who are able to file complaints about rights violations to include billing staff, receptionists and anyone else who in any way "assist[s] in the performance" of a procedure.

Complaints of such violations are relatively rare — for a decade, the office would receive an average of one complaint like this each year. Severino frequently pointed to a jump in those complaints to 343 last year as proving the need for this rule. He attributed that increase to a strong message from his office that they were "open for business" when it came to issues of religious freedom.

However, that increase in the number of complaints is "demonstrably false," according to Engelmayer's ruling. Nearly 80% of all the complaints given to the court were about vaccinations — unrelated to health care workers and their religious beliefs in providing care.

The judge writes that only 21 — or 6% — of the complaints that the government provided the court are even potentially related to providers' moral or religious objections. During oral arguments, the government's attorney conceded that the real number of complaints was "in that ballpark."

"This conceded fact is fatal to HHS's stated justification for the Rule," Engelmayer writes. "Even assuming that all 20 or 21 complaints implicated the Conscience Provisions, those 20 or 21 are a far cry from the 343 that the Rule declared represented a 'significant increase' in complaints."

In a statement to NPR, the government said, "HHS, together with DOJ, is reviewing the court's opinion and so will not comment on the pending litigation at this time."

Copyright 2021 NPR. To see more, visit https://www.npr.org.