WASHINGTON — Victims’ rights and women’s rights groups sued Education Secretary Betsy DeVos on Thursday, saying that rules that she issued last year to guide campuses on how to manage sexual assault complaints violated federal law and discriminated against accusers.

Three organizations, represented by prominent civil rights litigators, filed a complaint in the Northern District of California outlining ways that the guidance issued by Ms. DeVos in the fall had had a “chilling effect” on campus sexual assault investigations.

Since the guidance was issued, the groups charged, accusers have been less inclined to pursue sexual assault cases, and colleges have demonstrated a lack of urgency and clarity in pursuing them.

In September, Ms. DeVos rescinded Obama-era guidance on how colleges should manage the investigations under Title IX, the federal law that prohibits sex discrimination and governs the rules on investigating sexual assault on campus.