The Education Department confirmed Monday it is no longer investigating civil rights complaints from transgender students barred from school bathrooms that match their gender identity, a development those students say leaves them vulnerable to bullying and violence.

The Obama administration in 2016 directed public schools to allow students to use bathrooms that align with their gender identity, even if that conflicted with the gender on their birth certificates. The administration concluded that barring transgender students from public school bathrooms was a form of sex discrimination prohibited under Title IX.

But shortly after President Trump took office last year, Education Secretary Betsy DeVos and Attorney General Jeff Sessions rescinded the guidance, a move that was widely decried by civil rights groups who said it could endanger the welfare of transgender students. DeVos said states and individual school districts should be able to determine how to accommodate transgender students. They argued that Title IX did not obligate schools to allow transgender students to use the bathroom of their choice.

Transgender students say using the bathroom that feels right for them is essential for their safety and well-being and poses no threat to others. Some other students and their families see it as an affront to privacy and traditional values. It is a battle that has been waged at school board meetings, in state legislatures and in the courts. A transgender student from Virginia, Gavin Grimm, took his fight to use the boys’ bathroom to the U.S. Supreme Court in 2016. The high court declined to hear the case after DeVos reversed course on transgender students rights.

In the aftermath of the move, it remained unclear how the department would handle civil rights complaints from transgender students who were barred access to public school bathrooms. In June, Candice Jackson, the acting head of the Office for Civil Rights, told staff that it should evaluate civil rights complaints from transgender students on a case-by-case basis but did not say outright that bathroom complaints should be dismissed. That same month, the department dismissed a long-running civil rights complaint from a transgender girl in Ohio who had been barred from the girls’ bathroom at school.

Transgender students held out hope that the department would continue to back them when they raised issues about bathroom access, even though the guidance was no longer in place. Advocates maintain that Title IX, which bars sex discrimination in schools that receive federal funds, requires schools to allow transgender students to use bathrooms that match their gender identity. Some federal appeals courts have backed this view.

But the department interprets the law differently. It confirmed Monday that it will not investigate civil rights complaints from transgender students regarding bathroom access, though it will continue to scrutinize other forms of discrimination. The development was first reported by BuzzFeed.

“Title IX prohibits discrimination on the basis of sex, not gender identity,” Education Department spokeswoman Elizabeth Hill said in response to questions from The Washington Post. “Where students, including transgender students, are penalized or harassed for failing to conform to sex-based stereotypes, that is sex discrimination prohibited by Title IX. In the case of bathrooms, however, longstanding regulations provide that separating facilities on the basis of sex is not a form of discrimination prohibited by Title IX.”

Pressed on whether the department would investigate such complaints, Hill said: “Where [the Office for Civil Rights] does not have jurisdiction based on current law [the Office for Civil Rights] does not investigate.”

That aligns with the view held by some conservative legal groups, which have sued on behalf of students made uncomfortable by sharing restrooms with their transgender classmates, saying it violates student privacy.

But Catherine Lhamon, who headed the Education Department’s Office for Civil Rights under President Barack Obama, called the department’s statement “appalling and deeply dangerous.”

“The federal courts have multiple times made clear that Title IX protects transgender students,” Lhamon said. “They just don’t have the option to say, ‘We just don’t apply the law here.’ ”

DeVos has emphasized that her department would not tolerate bullying or harassment of transgender students, and Jackson’s memo made clear that the department would still investigate other kinds of discrimination against transgender students.

“Please note that the withdrawal of these guidance documents does not leave students without protections from discrimination, bullying or harassment,” DeVos wrote last year after she rescinded the Obama-era protections from transgender students. “All schools must ensure that all students, including LGBT students, are able to learn and thrive in a safe environment.”

Still, advocates worry that the administration’s position will send a message to schools without clear policies that they should bar transgender students from bathrooms and locker rooms that match their gender identity. “The vast number of schools in our country are schools led by teachers and principals and administrators who want to do the best for children but this will just be confusing,” said Vanessa Ford, the mother of a transgender girl in the first grade who attends school in the Boston area. “They hear this and think, ‘Wait, am I no longer allowed to support trans kids at our school?’ ”