LGBT rights groups are criticizing a federal judge's ruling blocking federal guidance on transgender bathroom use.

Within days after the Obama administration issued its guidance in May, a number of states led by Texas filed a federal lawsuit to block the rules from taking effect, arguing that transgender individuals are not protected under Title IX as maintained by the administration.

In a ruling issued Sunday, U.S. District Judge Reed O'Connor sided with the states and granted a nationwide injunction blocking the Department of Justice from enforcing the guidance until the lawsuit is settled.

(Related: Federal judge temporarily blocks Obama's transgender bathroom policy.)

“Judge O’Connor's decision to bar the Department of Justice from enforcing this important guidance puts thousands of transgender students at even greater risk of marginalization, harassment, and discrimination as they return to school this fall,” said Human Rights Campaign (HRC) Legal Director Sarah Warbelow. “All students, regardless of their gender identity, deserve to be able to learn in an environment free from discrimination. Despite this judge’s decision, schools are not barred from following the federal guidance, and school administrators still have a responsibility to ensure that the civil rights of all students are respected and that transgender students have access to facilities consistent with their gender identity. As lawsuits on the scope of Title IX proceed, we believe that justice will prevail as courts continue to recognize that discrimination against transgender students is a form of sex discrimination.”

Civil rights organization Lambda Legal, American Civil Liberties Union (ACLU), ACLU of Texas, National Center for Lesbian Rights (NCLR), Transgender Law Center and GLBTQ Legal Advocates & Defenders (GLAD) filed a joint amicus brief in support of the administration's position.

“A ruling by a single judge in one circuit cannot and does not undo the years of clear legal precedent nationwide establishing that transgender students have the right to go to school without being singled out for discrimination,” the groups said in a joint statement. “This unfortunate and premature ruling may, however, confuse school districts that are simply trying to support their students, including their transgender students. So let us make it clear to those districts: your obligations under the law have not changed, and you are still not only allowed but required to treat transgender students fairly. The scope of this injunction has no effect on the ability of other courts or lawyers representing transgender people to continue to rely on the federal government’s interpretations of Title IX or on prior decisions that have reached similar conclusions about the scope of federal sex discrimination laws.”

“The court's misguided decision targets a small, vulnerable group of young people – transgender elementary and high school students – for potential continued harassment, stigma and abuse,” they added.