Washington — The Supreme Court on Wednesday left intact a lower court decision that blocked the Trump administration from enforcing a new Bureau of Prisons policy that would end certain medical interventions for transgender inmates.

In an unsigned, one-line order, the high court rejected an emergency appeal from the Justice Department asking it to freeze the district court order and revive the new rules. The policy would cut off surgical and hormone therapy treatments, as well as social accommodations, for inmates who have been or will be diagnosed with gender dysphoria. 

Justices Samuel Alito and Clarence Thomas said they would have allowed the Trump administration to enforce the change.

The Trump administration sought the Supreme Court’s intervention in the dispute last month and argued that the new policy for transgender inmates is needed to “maintain institutional security.” 

But lawyers for a transgender woman and two transgender men in federal prisons who challenged the rules said the Bureau of Prisons has provided hormone treatment to people with gender dysphoria since 1992. They said that the new policy required the end of treatment for nearly 1,000 inmates in the bureau’s custody.

The dispute before the Supreme Court stems from a lawsuit the inmates filed against the Trump administration last year on behalf of incarcerated people diagnosed with gender dysphoria. The suit was filed after President Trump issued an executive order that barred the use of federal funds for medical procedures or treatments for transgender inmates who are in Bureau of Prisons custody.

In response to Mr. Trump’s directive, the Bureau of Prisons issued a new policy in February stating that it would not provide surgeries or hormone therapy to address gender dysphoria. Inmates who were receiving hormone treatments could be put on a tapering plan that would eventually lead to a discontinuation of the interventions.

Under the new rules, the Bureau of Prisons will also no longer provide any social accommodations, such as breast padding, binders, wigs and makeup, to inmates with gender dysphoria.

In a memo accompanying the policy, the Bureau of Prisons cited Mr. Trump’s executive order and said it changed its rules to “reflect treatment for gender dysphoria that is more aligned with the latest scientific information, that is consistent with BOP’s longstanding policy of providing medical care that is tailored to the unique needs of the inmate, and that accounts for the complex security and administration concerns in the correctional environment.”

In June, U.S. District Judge Royce Lamberth issued an order preventing the Trump administration from enforcing the February policy. The judge required the Bureau of Prisons to continue providing medical interventions and social accommodations to a class of inmates with gender dysphoria.

“The court does not wade into the culture war being waged against transgender individuals,” Lamberth, who was appointed by President Ronald Reagan, wrote in a 31-page decision. “The court simply concludes that the government violated [federal law] when it issued a new policy restricting the provision of gender-affirming care to inmates diagnosed with gender dysphoria.”

Lamberth issued an order in August that continued to block the policy.

A three-judge panel of the U.S. Court of Appeals for the District of Columbia Circuit then declined to lift the district court’s injunction. In a 2-1 decision, the appeals court said the Bureau of Prisons “did not adequately consider its own experience providing gender-affirming care under its prior policy” and failed to make a strong showing that it is likely to succeed on the merits of the case.

In its emergency appeal to the Supreme Court, Solicitor General D. John Sauer argued that the district court’s decision “prevents the application of the Executive’s chosen policy” on a broad basis.

Sauer defended the legality of the policy ending medical treatments for transgender inmates and said the Bureau of Prisons “seasonably considered its prior experience both in determining that such interventions are not medically necessary and in determining that security and prison-administration concerns independently justified a change in policy.”

But the challengers of the administration’s new rules argued the Trump administration failed to put forth any evidence indicating whether healthcare providers for the Bureau of Prisons found the now-restricted medical treatments to be effective, ineffective or harmful.

“BOP cut off treatment that its healthcare providers had recommended for decades and replaced it with psychotherapy — which its own expert acknowledges is backed by no evidence demonstrating its efficacy as a treatment for gender dysphoria — and psychotropic medications — which BOP’s Medical Director does not even claim treat gender dysphoria, only co-existing conditions,” lawyers for the transgender inmates wrote.

They also argued that the agency has not “pointed to a single security incident” relating to the provision of medical interventions to address gender dysphoria.

“Had BOP’s doctors found this treatment unhelpful or harmful to patients or had the agency found that the treatment compromised security, surely BOP would have mentioned it in the administrative record,” lawyers for the plaintiffs said. “That glaring omission, as well as the unreasonableness of its decision, make it clear that the rationales were contrived to support the demand President Trump made in the EO.”