This month, regional battles over the right of transgender people to access public bathrooms were elevated to national legal theatre. First, the Justice Department told North Carolina that its recent law, requiring education boards and public agencies to limit the use of sex-segregated bathrooms to people of the corresponding biological sex, violated federal civil-rights laws. Governor Pat McCrory responded with a lawsuit, asking a court to declare that the state’s law doesn’t violate those federal laws. Meanwhile, in a suit filed on the same day, the Justice Department asked a court to say that it does.

To top it off, on May 13th the Education Department’s Office for Civil Rights (O.C.R.) and the Justice Department’s Civil Rights Division issued a Dear Colleague letter announcing to the nation’s schools that, under Title IX—the 1972 law banning sex discrimination by schools that receive federal funding—transgender students must be allowed to use rest rooms that are “consistent with their gender identity.” The threat was clear: schools that failed to comply could lose federal funding. Protests of federal overreach immediately ensued, including from parents citing safety and privacy as reasons for children and teen-agers to share bathrooms and locker rooms only with students of the same biological sex.

In chastising North Carolina, the Justice Department explained that if non-transgender people may use bathrooms consistent with their gender identity, then denying transgender people access consistent with their gender identity constitutes discrimination on the basis of sex. Similarly, the Dear Colleague letter states that the federal government “treats a student’s gender identity as a student’s sex for the purposes of Title IX.” These interpretations of federal anti-discrimination law are new and surprising. It is not at all obvious that the “sex” in sex-discrimination law means not sex but gender, let alone “an internal sense of gender,” as the Letter says. But it is also reasonable to interpret sex-discrimination law to prohibit discrimination against transgender people. Given that single-sex bathrooms have never been seen as constituting sex discrimination, the tricky question is whether limiting them based on biological sex, rather than gender, does indeed discriminate on the basis of sex.

Quite apart from a possible legal right, it is reasonable to think that the appropriate bathrooms for transgender people to use are ones fitting their gender identities. But the parents’ rhetoric of federal overreach on Title IX is not off base. It is of course unexceptional for the federal government to enforce federal law. But, unlike the Education Department’s many regulations, the Dear Colleague letter is not law, because it wasn’t enacted through legal procedures, involving public input, that federal agencies must follow when making law. The Education Department’s rule that schools must provide prompt and equitable grievance procedures to hear complaints of Title IX sex discrimination results from that required process and is legally binding. But the agency chose not to have such a process for its missive on transgender students.

This is a familiar but controversial O.C.R. strategy. Its last Dear Colleague letter about Title IX, in 2011, said that sexual violence is a form of sexual harassment and is therefore sex discrimination. It detailed how colleges and universities must discipline perpetrators and prevent such incidents. It too came with a threat to cut off federal funds, and O.C.R. proceeded to investigate hundreds of schools for noncompliance. (O.C.R. found Harvard Law School, where I teach, in violation of certain terms of the Dear Colleague letter. I have been critical of the federal pressure on schools to adopt policies and procedures that deny fairness to accused students in the name of Title IX compliance.) Several lawsuits claiming that O.C.R. unlawfully promulgated and enforced the contents of its Dear Colleague letter on sexual violence are currently pending in the federal courts.

Whether or not the federal government acted unlawfully, it has now set in motion a potential Title IX collision course between its directives on sexual violence and on bathrooms. Schools attempting to comply with the federal bathroom policy have at least two possible ways of doing so: allow students to use sex-segregated bathrooms and locker rooms based on their gender identity, or move away from sex segregation of such facilities. The latter, gender-inclusive arrangement, which was in place in my college dormitory more than twenty years ago, is not uncommon on campuses, and a social movement to desegregate at least some portion of bathrooms is growing. Some colleges have made every bathroom on campus open to any gender, and this solution could well become a practical choice at K-12 public schools.

But there is also a growing sense that some females will not feel safe sharing bathrooms, shower rooms, or locker rooms with males. And if a female student claimed that a bathroom or locker room that her school had her share with male students caused her to feel sexually vulnerable and created a hostile environment, the complaint would be difficult to dismiss, particularly since the federal government has interpreted Title IX broadly and said that schools must try to prevent a hostile environment. This is not wholly hypothetical. Brandeis University found a male student responsible for sexual misconduct for looking at his boyfriend’s genitals while both were using a communal school shower. The disciplined student then sued the school for denying him basic fairness in its disciplinary process, and a federal court recently refused to dismiss the suit.

Continuing to have segregated bathrooms could also put schools in a bind on Title IX compliance. According to the federal government, a transgender girl who is told to use the boys’ locker room, or even a separate and private stall, instead of the girls’ facility, has a claim that the school is violating Title IX. A non-transgender girl who’s told she must share a locker room with boys may also have a claim that the school is violating Title IX. But would she not have a similar claim about having to share with students who identify as girls but are biologically male? Well, not if her discomfort and “emotional strain” should be disregarded. But this week, in a letter, dozens of members of Congress asked the Attorney General and the Secretary of Education to explain why they should be disregarded. The federal government is putting schools in a position where they may be sued whichever route they choose. (Catherine Lhamon, the assistant secretary for Civil Rights at the Department of Education, declined to comment on this issue.)

The debate around which bathrooms transgender people should use has given rise to deeper questioning of why we even have a norm of gender segregation for bathrooms in the first place. But a push to make those spaces open to all genders comes up uneasily against feelings of female sexual vulnerability and their effect on an equal education or workplace. To make things more complicated, the risk of sexual assault and harassment of transgender females in male bathrooms is a salient reason for providing access to bathrooms according to gender identity, while many worry about transgender males being sexually bullied in male bathrooms.

The common denominator in all of these scenarios is fear of attacks and harassment carried out by males—not fear of transgender people. The discomfort that some people, some sexual-assault survivors, in particular, feel at the idea of being in rest rooms with people with male sex organs, whatever their gender, is not easy to brush aside as bigotry. But having, in the past several years, directed the public toward heightened anxiety about campus sexual assault, the federal government now says that to carry that discomfort into bathrooms is illegitimate because it is discrimination. The sense that the Education Department has not looked down the road to consider the conflict is only confirmed by its penchant for announcing bold and controversial rules in letters, rather than through lawful processes.