LOS ANGELES — The University of Southern California mishandled reports that former student health center gynecologist George Tyndall repeatedly sexually assaulted female patients, which may have allowed abuse to continue for years, a federal investigation concluded.

The findings released Thursday by the U.S. Department of Education’s civil rights office were the result of what federal officials described as one of the most intense probes conducted of a college’s handling of sexual misconduct, involving interviews with more than 90 people.

“This total and complete failure to protect students is heartbreaking and inexcusable,” Education Secretary Betsy DeVos said in a statement. “Too many at USC turned a blind eye to evidence that Dr. Tyndall was preying on students for years.”

The findings further detail that the university’s top brass knew about serious allegations against Tyndall while it was already under investigation by the department over student allegations that USC mishandled sexual assault cases in late 2017 but failed to disclose them to federal agents.

“We are certainly very disappointed by the responsiveness of the University of Southern California in this case,” said Kenneth Marcus, assistant secretary of civil rights for the department.

When asked by NBC News if department officials believe USC engaged in a cover-up of allegations against Tyndall, Marcus said: “It is difficult to determine with certainty whether documents were withheld with intention.”

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Tyndall has been accused of sexual abuse by nearly 400 women while employed at the private university in Los Angeles. He pleaded not guilty last year to criminal charges of sexually abusing 16 patients.

USC failed to investigate warnings from at least nine patients about Tyndall’s conduct between 2000 and 2009, the department found, and it failed to look into complaints in 2016 that he conducted pelvic examinations without gloves.

Also in 2016, the university discovered over 200 photos of patients’ genitals in Tyndall’s office but didn’t investigate that either and allowed him to continue seeing patients, according to the department. There were more photos that Tyndall admitted to taking with a Polaroid camera as far back as 1989, but the university didn’t take steps to locate them, the federal investigation concluded.

The department opened an investigation into USC’s handling of allegations against Tyndall in May 2018 following a Los Angeles Times investigation and just two months after concluding a similar Title IX inquiry of the university.

Multiple students had filed complaints with the Education Department during the Obama administration, prompting a years-long federal investigation that concluded in March 2018. The department cleared the university of violating Title IX in a few specific cases it reviewed but also found the university sometimes took months to issue decisions on cases, failed to tell students about all their rights in sexual misconduct cases and didn’t always detail how long investigations would take. The university agreed to a number of reforms that the department would monitor.

By the time the university announced an agreement with the federal government to end the earlier Title IX investigation in March 2018, the allegations against Tyndall had become so significant that the president was briefing trustees about it. However, the university still hadn’t told the Education Department about the situation.

According to the department, USC’s president and provost insisted to federal officials that they didn’t know much about the allegations against Tyndall other than what the university’s general counsel’s office told them — that the doctor’s misbehavior involved harassing words and outdated medical practices.

Under an agreement reached with the department this week, USC will have to create a centralized record-keeping system to track misconduct complaints against employees and what actions school officials take in response to them.

The university will also have to contact nine patients who complained of misconduct by Tyndall and "offer to remedy any sex discrimination caused" by Tyndall, investigate whether people who reported Tyndall faced retaliation and further review whether current and former employees took appropriate steps responding to warnings about the doctor.

USC President Carol Folt said in a statement that the university will follow the department's orders, and that the school "is confronting its past and implementing changes necessary to inform its future."

The university has agreed to a $215 million class action settlement to split among over 18,000 women who saw him as patients.