The rule would allow any health care worker or entity to deny medical treatment, information and services to patients because of personal religious or moral beliefs.
"The Court vacates the 2019 rule in its entirety", US District Judge Paul Engelmayer wrote in an opinion Wednesday, noting that existing federal conscience provisions "accommodate religious and moral objections to health care services provided by recipients of federal funds" and "recognize and protect undeniably important rights".
Proposed by HHS' Office of Civil Rights more than a year ago, the rule was created to protect "conscience rights" of health-care providers by boosting enforcement of at least two dozen laws already on the books that allow doctors, nurses, technicians, and other providers to opt out of procedures such as abortions or gender-change procedures to which they object.
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.
The U.S. Justice Department and HHS didn't respond to the Washington Blade's request to comment on the decision immediately after it was handed down.
Two federal judges in two days have struck down the Trump administration's Denial of Care rule as a third case in San Francisco awaits a judge's decision.
HHS declined to comment on the judge's decision.
"Two judges in two days have recognized the Denial of Care rule for what it is, an egregious and unconstitutional attack on women, LGBT people, and other vulnerable populations", said Jamie Gliksberg, Lambda Legal senior attorney.
"Today, the court safeguarded the public's health by striking down the Trump administration's healthcare refusal rule", Clare Coleman, president and CEO NFPRHA said in a statement.
"There is no place for discrimination in health care, and we will continue our work to prevent the Trump administration from illegally wiping out decades of progress when it comes to patient care", Herrera wrote. "Freedom of religion is a fundamental right, but it can not be used to harm others", the ACLU said.
New York Attorney General Letitia James, who led the coalition that filed the lawsuit, said the judge invalidated the law and blocked it from taking effect.
At a time when the future of reproductive rights is uncertain, further restricting access to reproductive healthcare in the name of religious freedom would be especially harmful to patients, said the group Physicians for Reproductive Health.
HHS cites 358 complaints between November 2016 and the end of fiscal year 2018, but Engelmayer notes the Trump administration has admitted six percent are duplicates, leaving only 343, and "only around 20 complaints implicate any of the conscience provisions".