In January, a federal judge in Los Angeles signaled that he was inclined to approve the University of Southern California’s $215 million class-action settlement with former patients of Mr. Tyndall, who was charged criminally in June 2019 with 29 total counts of sexual penetration and sexual battery. If convicted, he could face up to 53 years in prison. He has denied wrongdoing.

Kenneth L. Marcus, the assistant secretary of education for civil rights, said the investigation was one of the largest that the office had ever conducted. The department initiated the investigation itself, a rare step, in May 2018 based on concerns that had arisen during previous investigations at the school. Investigators reviewed 20,000 pages of documents, interviewed about 95 staff and students, and held a community meeting.

Mr. Marcus said the investigation turned up “extraordinarily egregious” facts in one of the “most shocking cases we’ve seen.” Investigators determined that the university was notified about sexual harassment since at least 2000, and that “its failure may have allowed female students to be subjected to such discrimination for more than a decade.”

They found that patients and staff complained that during pelvic examinations, Mr. Tyndall made inappropriate remarks about physical attributes; that he would conduct pelvic exams without gloves; and in 2016, that the university failed to investigate more than 200 photographs of patients’ genitals that were discovered in his office.

Carol Folt, the university’s president, said in a statement that the agreement reflected its commitment to “work in partnership” with the Education Department’s Office for Civil Rights “to further a culture and climate where students, faculty and staff can learn, work and thrive,” and that the university had already taken several steps to improve.