A federal appeals court heard oral arguments Wednesday in a case involving Catholic entities attempting to exempt themselves from a federal requirement that they insure or provide gender-transition procedures that violate their religious beliefs.

The years-long dispute emerged after the Obama administration in 2016 interpreted the Affordable Care Act's ban on sex discrimination as applying to gender identity and termination of pregnancy. The Trump administration moved to grant religious exemptions, and two courts struck down the Obama-era mandate, but the Biden administration is appealing those rulings.

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Little Sisters of the Poor wait for U.S. President Donald Trump to speak during a "Make America Great Again" rally at Total Sports Park Nov. 1, 2020, in Washington, Mich. (BRENDAN SMIALOWSKI/AFP via Getty Images)

Opposing the administration's appeal is an order of nuns known as the Sisters of Mercy, the University of Mary and a Catholic health care company known as SMP Health System. 

The Becket Fund, a conservative legal nonprofit representing those groups, contends that the Department of Health and Human Services (HHS) is violating the Religious Freedom Restoration Act (RFRA) by forcing compliance with this rule.

CHILDREN'S CHARITY SUING HHS FOR REVOKING WAIVERS FOR FAITH-BASED ORGANIZATIONS

In response, HHS has argued that those groups lack standing because the department hasn't attempted to enforce the regulation against them. "The central flaw" in a lower court's decision, according to an HHS filing, "is straightforward: The court enjoined the government from enforcing the statutes in a way that the government has not to date indicated it will enforce them."

Health and Human Services Secretary Xavier Becerra speaks during a World AIDS Day commemoration in the East Room of the White House in Washington, D.C., Dec. 1, 2021. (MANDEL NGAN/AFP via Getty Images)

"Because plaintiffs' claims are rooted in speculation, plaintiffs lack standing, their claims are not ripe and they have not demonstrated imminent irreparable harm necessary to justify permanent injunctive relief."

Luke Goodrich, vice president and senior counsel at the Becket Fund, said Wednesday that the HHS rule was bad for doctors and religious liberty.

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"Both federal courts to consider this controversial mandate have struck it down as bad for patients, bad for doctors and bad for religious liberty," Goodrich said. "It is past time for this administration to stop forcing doctors to go against conscience and sound medical judgment and to start respecting their Hippocratic Oath to ‘do no harm.’"

HHS did not immediately respond to Fox News' request for comment.