U.S. District Judge Paul A. Engelmayer said the U.S. Health and Human Services Department overstepped its authority and went beyond existing law in issuing the rule. He also said that the measure could be costly, burdensome and damaging to emergency care and that the whole rationale for the rule was based on a lie.
He said the department's claim that there was a significant increase in complaints about workers being forced to violate their conscience was "flatly untrue." The HHS rule, he said, is a classic "solution in search of a problem."
An HHS spokeswoman had no comment.
Nineteen states, the District of Columbia, three local governments, health organizations and others had sued to block the rule from taking effect Nov. 22, arguing that it would be discriminatory and would interfere with people's access to health care.
"Today, the Trump administration has been blocked from providing legal cover for discrimination," said Alexis McGill Johnson, acting president of Planned Parenthood. "As the federal district court made clear, the administration acted outside its authority and made false claims to try to justify this rule."
Rosie Phillips Davis, president of the American Psychological Association, said the HHS rule "could have jeopardized the health of some of our most vulnerable populations, including women, LGBT people and people with HIV or AIDS."
But Sen. Ben Sasse, a Nebraska Republican, called the ruling "absurd mush" and urged the Trump administration to appeal.
Health care institutions have long relied on federal Conscience Provisions first created in 1973 and amended since then that protected health care professionals from carrying out services that conflict with their religious or moral beliefs.
The new HHS rule broadens the list of health care personnel who can refuse to participate, expanding it to those who counsel, refer, train or make arrangements for a medical procedure.
It also restricts the ability of employers to inquire about employees' objections and broadens the definition of health care entities to include pharmacists and medical laboratories.
Thus, the judge warned, a hospital or clinic receptionist who schedules appointments, an elevator operator or an ambulance driver could refuse on moral or religious grounds to do their jobs.
He said the rule could force some health care employers to double or triple staff, particularly during emergencies.
"These limits have clear potential to inhibit the employer's ability to organize workplace arrangements to avoid inefficiencies and dislocations," Engelmayer said.
Engelmayer, who was appointed by Democratic President Barack Obama, said HHS lacked authority to create major portions of the rule, including a provision that said a health care institution's federal funding can be cut off for violating the measure.
He said it should be left to Congress to decide whether to change the laws regarding employers' duty to accommodate religious objections.