Two prominent Catholic bishops on Monday denounced President Obama’s order compelling public schools to allow restroom and locker room use on the basis of gender identity rather than sex.

The statement, issued by Bishop Richard Malone of Buffalo and Archbishop George Lucas, who are both committee chairmen of the U.S. Conference of Catholic Bishops, cites church teaching reiterated by Pope Francis last month in his apostolic exhortation Amoris Laetitia.

“The guidance issued May 13 by the U.S. Department of Justice and U.S. Department of Education that treats ‘a student’s gender identity as the student’s sex’ is deeply disturbing,” the bishops said in a statement. “The guidance fails to address a number of important concerns and contradicts a basic understanding of human formation so well expressed by Pope Francis: that ‘the young need to be helped to accept their own body as it was created.’ “

The bishops said no student should ever be made to feel unsafe, but they contended the order curtails “more just and compassionate approaches” for students struggling with their gender identity.

“It unfortunately does not respect the ongoing political discussion at the state and local levels and in Congress, or the broader cultural discussion, about how to address these sensitive issues,” the bishops said. “Rather, the guidance short-circuits those discussions entirely.”

Mr. Obama’s order on Friday informed public schools of “emerging practices” about how to regulate bathrooms and locker rooms for transgender students. It advocates regulating bathrooms and locker rooms on the basis of gender identity, rather than sex, and installing privacy curtains in changing rooms when applicable.

The letter is legally nonbinding, but could threaten federal education funds for schools that do not comply.

The bishops said they are “studying the guidance further to understand the full extent of its implications.”

The 25-page guidelines came in response to a heated national debate sparked by a North Carolina law regulating public facilities on the basis of sex. The U.S. Department of Justice sued North Carolina last week over the statute, saying it violates federal civil rights law.

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