The Office for Civil Rights said that it sent letters under its authority to enforce Title VI of the Civil Rights Act, which bans any institution receiving federal funds from discriminating based on race, color, and national origin.
Stanford and UC Berkeley are among the schools.
The announcement comes amid mounting pressure on university administrators to rein in pro-Palestinian demonstrations, which have erupted periodically on college campuses across the country over the past year and led to the arrest of hundreds of demonstrators.
President Donald Trump's administration has made combating what it considers anti-Israel and antisemitic movements on college campuses a priority.
RELATED: UC Berkeley protest joins fight to release detained Columbia activist amid funding cuts threats
He signed an executive order during his second week in office to "combat antisemitism" in schools and on university campuses, and on February 3 announced the creation of a multi-agency task force to carry out the mandate.
Trump also vowed to cut federal funding to colleges accused of tolerating antisemitism, announcing last week that Columbia would be the first target.
Education Secretary Linda McMahon described the protests as "attacks" on Jewish students and faculty in an interview on CNBC on Tuesday, adding that Trump "has been incredibly clear that he is not going to tolerate that kind of attacks on campuses and that he will defund those universities."
The Trump administration announced Friday the cancellation of $400 million in federal grants and contracts to Columbia -- citing what it described as the school's failure to quash antisemitism on campus. It's unclear which parts of the university's research and activities will be affected.
McMahon said she spoke with Columbia University Interim President Katrina Armstrong last week. In that conversation, McMahon said she noted the issue "seemed to be systemic" and advised the university to "look at faculty and what they were teaching" to see whether they were encouraging unrest, and vet international students.
"Are these students who are going to be looking to participate in riots? Are there outside agitators that come on campus?" McMahon said. "This is not a freedom of speech issue. This is a safety and civil rights issue."
Before Monday's announcement, the Department of Education had said in early February that it was investigating UC Berkeley and four other universities on the list: Columbia; Northwestern University; Portland State University; and the University of Minnesota Twin Cities.
RELATED: CAIR labels Stanford a 'hostile campus' for stance on pro-Palestinian protests
CAIR: Stanford a 'hostile campus' for stance on pro-Palestine protests
The 55 other universities are now under investigation or are being monitored "in response to complaints filed with OCR," according to Monday's statement.
Six of the eight Ivy League universities received letters, including Columbia University and Harvard University.
"The Department is deeply disappointed that Jewish students studying on elite U.S. campuses continue to fear for their safety amid the relentless antisemitic eruptions that have severely disrupted campus life for more than a year. University leaders must do better," McMahon said in a statement last week.
Columbia has been at the forefront of US campus protests against the war in Gaza since last spring, with protesters rallying against Israel's military action in Gaza following the October 7, 2023, Hamas-led attacks and calling for universities to sell investments in companies tied to Israel or the war.
Pro-Palestinian demonstrators at Columbia set up a weekslong encampment on college grounds last April and went on to occupy a campus building before riot police cleared the building and arrested dozens of students. Some of those cases were later dismissed in court.
Pro-Palestinian protesters have repeatedly said there's nothing antisemitic about criticizing Israel over its actions in Gaza or expressing solidarity with Palestinians and calling for a ceasefire.
Last week, Mahmoud Khalil, a Palestinian activist who helped lead Columbia's student protest movement, was arrested by federal immigration officers who said they were acting on a State Department order to revoke his green card, according to his attorney.
RELATED: Charges dropped against Stanford student journalist who was covering barricaded protest last year
He was among those under investigation by a new university committee that brought disciplinary charges against dozens of students for their pro-Palestinian activism, according to The Associated Press.
Trump, in a post on Truth Social, described Khalil's detainment as "the first arrest of many to come" amid a wider crackdown on foreign students who participated in what the president said were "illegal protests" against the war in Gaza.
On Monday, a federal judge in New York blocked efforts by the Trump administration to deport Khalil until a hearing on Wednesday so the court can consider the lawsuit challenging his detention.
"ICE's arrest and detention of Mahmoud follows the US government's open repression of student activism and political speech, specifically targeting students at Columbia University for criticism of Israel's assault on Gaza," Khalil's attorney Amy Greer said.
"The US government has made clear that they will use immigration enforcement as a tool to suppress that speech."
It's unclear how long many of the institutions have been under investigation, but the Office for Civil Rights on Friday directed its personnel to prioritize addressing a "backlog" of complaints alleging antisemitic violence and harassment.
ABC7 News contributed to this report.
(The-CNN-Wire & 2024 Cable News Network, Inc., a Time Warner Company. All rights reserved.)