What has become a national uprising against the scourge of sexual assault on college campuses started three years ago with a 19-page letter from an obscure agency in Washington.

Sexual violence was not only a crime that could land a perpetrator in jail, the Office for Civil Rights in the Education Department told schools in April 2011. It was also a form of harassment prohibited by federal anti-discrimination law, a declaration that required colleges to take vigorous steps to prevent sexual violence and provide a “prompt and equitable” response whenever cases arose.

The letter from the Obama administration helped encourage survivors of rape and other forms of sexual assault to lodge grievances with the federal government, with widening consequences for higher education.

“It was the first time any administration had called out sexual violence as a civil rights issue,” Catherine E. Lhamon, assistant education secretary for civil rights, said of the letter. “It was a shot across the bow.”

From October through April, Lhamon’s office received 43 civil rights complaints related to sexual violence at colleges. That’s about four times as many as the office received in the entire fiscal year of 2010.

Expanded civil rights enforcement is one of several ways the administration has pressed to tighten oversight of higher education. The department aims to force changes at for-profit colleges that leave graduates with too much debt and poor job prospects. It also is developing a plan to rate colleges on value and access. Both of those initiatives are controversial, but the sex-assault initiative has drawn huge attention.

Sexual assault has plagued colleges for generations. Administrators who faced the problem often tried to keep it a private matter, resolved behind closed doors with minimal campus disturbance. Now the issue has gone public. In January, President Obama asked a task force to develop ways to protect students from sexual violence.

On Thursday, the department made public for the first time a list of colleges under investigation for possible violations of the 1972 law known as Title IX, stemming from their handling of sexual violence and harassment complaints. Of the 55 institutions listed, three were subject of investigations predating the letter: Harvard Law School, Princeton University and Ohio State University. The rest came under federal scrutiny afterward, officials said, with most of the cases the result of a mounting number of student complaints.

Lhamon hastened to point out that the release of the list did not mean any of the 55 schools broke the law. But in a higher-education market sensitive to public perceptions, with schools constantly angling to get noticed through one national ranking or another, this is one list they want to avoid.

“What colleges have today that’s most valuable for their franchise is their brand,” said James R. Marsh, a New York attorney who represents sex-assault victims. When sexual-violence questions hang over a school, he said, it “seriously undermines and hurts the brand.”

Marsh and Boston attorney Wendy Murphy represent a University of Virginia graduate who filed a federal civil rights complaint in 2012, alleging that U-Va. mishandled her report that she had been drugged and then raped by a classmate in December 2011. Separately, the Office for Civil Rights, known as OCR, had begun an investigation in June 2011 of possible civil rights violations related to sexual violence at U-Va.

Why that investigation remains open, nearly three years later, is unclear. Neither the Education Department nor U-Va. would comment on it.

But U-Va.’s associate dean of students, Nicole Eramo, said Friday that the university took numerous steps to bolster its policies on sexual violence after the OCR letter in 2011. The school broadened its definition of sexual misconduct to cover any unwelcome sexual behavior that occurs without effective consent; rules were clarified to ensure, for instance, that students know it is forbidden to drug someone for the purpose of sexual exploitation; and the policy was expanded to cover misconduct off, as well as on, the campus known as the Grounds.

Significantly, U-Va. adopted a new standard of proof that year for determining whether a student committed sexual misconduct. Instead of requiring “clear and convincing evidence” for finding a violation, the university determined that it would accept a lower standard of proof known as “preponderance of the evidence.” That shift followed direction from the OCR letter.

Some colleges, federal officials say, have resisted adopting the preponderance standard, contending that it does not adequately preserve the rights of the accused.

Eramo, who chairs a board of faculty, staff and students that hears sexual-misconduct cases, said the board has handled five formal complaints this school year and five informal complaints. The informal ­cases, she said, don’t lead to disciplinary action but do provide students with a secure forum to discuss painful incidents.

U-Va. has three staff members who investigate sexual misconduct, and Eramo said she would like to hire another because the ­cases are so complex. The university also is aiming to hire a coordinator for sexual-misconduct prevention.

“We’ve really tried to shift some of our focus from policy to prevention,” Eramo said.“I spend a lot of my time in react mode, and we want to be more proactive.”

The list of 55 schools under active investigation also included Frostburg State University in Western Maryland, with a case that opened Sept. 18; Catholic University in the District, with a case that opened Jan. 8; and the College of William and Mary in Williamsburg, with a case that opened April 18. All three schools pledged cooperation with authorities but declined to discuss details.

“From a purely public relations standpoint, we would rather not be on the list,” William and Mary spokesman Brian Whitson said. “But we’re not looking at this from a public relations perspective. . . . This is an issue we are very focused on. When it comes to response and education related to sexual violence, we spend a lot of time considering what we do and why we do it. We didn’t ask for this review, but we do expect to learn something along the way.”

Usually universities keep quiet any objections they might have about civil rights enforcement. On Monday, however, an open split emerged between Tufts University and OCR. The private university in Massachusetts, which had been under investigation for its handling of a 2010 sexual-assault case, acknowledged that “more could have been done” to address concerns of the student who made the report. But Tufts revoked an agreement it had reached with OCR in mid-April to resolve the issue, disputing a federal finding that the university’s current policies fell short of what the law required.

That leaves the school at odds with an agency that has the power to cut off its federal funding.

“We could not, in good faith, allow our community to believe that we were not in compliance with such an important law,” Tufts said in a statement. “Our goal is a campus culture in which every member of our community is respected, supported and safe. Sexual misconduct has absolutely no place at Tufts University.”