A federal court in Texas has blocked the Obama administration’s order compelling public schools nationwide to regulate restroom and locker room access on the basis of gender identity rather than biological sex.

In his ruling halting the edict, U.S. District Judge Reed O’Connor said the administration failed to comply with federal rule-making procedures in violation of the Administrative Procedures Act.

The court sided with Texas and 13 other states that sued the federal government over the order, arguing that the mandate overstepped federal authority and misinterpreted Title VII and Title IX, which bar sex discrimination in employment and education, respectively.

Texas Attorney General Ken Paxton said he was “pleased that the court ruled against the Obama administration’s latest illegal federal overreach.”

“This president is attempting to rewrite the laws enacted by the elected representatives of the people, and is threatening to take away federal funding from schools to force them to conform,” Mr. Paxton said in a statement. “That cannot be allowed to continue, which is why we took action to protect states and school districts, who are charged under state law to establish a safe and disciplined environment conducive to student learning.”

Judge O’Connor, who was appointed to the federal bench by President George W. Bush in 2007, said the Obama administration ran afoul of the Administrative Procedures Act by not including notice and comment.

He said in a ruling signed Sunday and made public Monday morning that the federal government’s interpretation of the anti-discrimination laws also flew in the face of the plain meaning of the statutes.

The judge pointed out that Title IX’s implementation regulation explicitly authorizes restrooms to be regulated on the basis of biological sex.

Judge O’Connor also applied his decision to enjoin the Obama order nationwide.

The ruling stems from an Obama administration edict in May compelling public schools across the nation to grant transgender students access to bathrooms, locker rooms and shower facilities corresponding with their gender identity. Noncompliant schools ran the risk of losing federal education funding.

The Obama administration argued that the order was only advisory and therefore not subject to rules under the Administrative Procedures Act. The judge threw out this argument, pointing to threats to pull federal education funding from noncompliant schools and a lawsuit attempting to force North Carolina to comply with the administration’s interpretation.

Roger Severino, director of The Heritage Foundation’s DeVos Center for Religion and Civil Society, said the ruling properly checked the Obama administration’s federal overreach.

“Although the federal government has discretion in how it interprets law, to be sure, it cannot make substantive new rules that have binding effect without following proper procedures, which includes notice and comment, which are the standard regulatory rule-making laws that are binding on all administrative agencies,” Mr. Severino said on a press call.

White House press secretary Josh Earnest said the administration will respect the ruling. “We’ve got a lot of confidence in the guidance that was put forward,” Mr. Earnest said.

“It certainly was not a mandate,” he said of the Education Department’s guidance. “I know it was described that way by some of our critics. The focus of the administration has been on practical problem-solving.”

Mr. Earnest said the administration’s goal always has been to provide a safe and dignified environment for students to learn.

Justice Department spokeswoman Dena Iverson said the agency is disappointed in the ruling and is considering its legal options.

Sarah Warbelow, legal director for the Human Rights Campaign, said the order “puts thousands of transgender students at even greater risk of marginalization, harassment, and discrimination as they return to school this fall.”

“All students, regardless of their gender identity, deserve to be able to learn in an environment free from discrimination,” Ms. Warbelow said in a statement.

Other states included in the lawsuit are Alabama, Arizona, Georgia, Kentucky, Louisiana, Maine, Mississippi, Oklahoma, Tennessee, Utah, West Virginia and Wisconsin.

The ruling comes amid a heated national debate about how the public should accommodate transgender individuals for the purpose of sex-specific intimate facilities.

A separate coalition of 10 states is also suing the Obama administration over the order. A group of 51 Chicago-area families filed a lawsuit in May challenging the administration’s interpretation of the laws.

The Supreme Court this month granted a temporary injunction blocking an order that would have allowed a biologically female student to use the boys’ restroom. The U.S. Department of Justice and North Carolina also filed dueling lawsuits in May over a state law regulating public facilities on the basis of biological sex.

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