San Jose State University has agreed to pay $1.6 million to 13 female student-athletes whose complaints about being sexually assaulted by an athletic trainer were mishandled by the university, federal prosecutors said Tuesday.

The payment is part of a settlement between the university, the U.S. Justice Department’s Civil Rights Division and the U.S. Attorney’s Office for the Northern District of California, which conducted a Title IX investigation that found the university failed to adequately respond to reports of sexual harassment and assault that started in 2009, exposing additional student-athletes to harm for over a decade.

Federal investigators also found the university retaliated against two employees, including one who repeatedly alerted school officials about the trainer. Female swimmers said he subjected them to repeated, unwelcome sexual touching of their breasts, groins, buttocks and pubic areas during treatment in the campus training facilities, federal prosecutors said.

“With this agreement, San José State University will provide relief to survivors and transform its Title IX process to ensure accountability in its athletics program and create a safer campus for all its students,” said Assistant Attorney General Kristen Clarke of the Justice Department’s Civil Rights Division.

University officials said they cooperated fully with the investigation by the Department of Justice and that the findings by federal prosecutors are similar to what an external investigation ordered by the university in 2019 and completed earlier this year found about the allegations against former Director of Sports Medicine Scott Shaw.

Both investigations identified 23 student-athletes who were inappropriately touched by Shaw but of those, only 13 have accepted to receive $125,000 each, the university said.

“We thank all the individuals who courageously came forward during the investigations. To the affected student-athletes and their families, we deeply apologize,” university officials said in a statement.

In April, Mary Papazian, president of San Jose State University, said in a campuswide letter to students, faculty and staff members that the external investigation found that the allegations were substantiated and that more recent allegations were raised in the course of the investigation.

Shaw resigned last year after allegations that from 2006 to 2009 he inappropriately touched swimmers during physical therapy resurfaced in the news media. He has denied misconduct, and no criminal charges have been filed against him.

Shaw’s attorney, Lori Jeanne Costanzo, didn’t immediately return a call seeking comment.

As part of the settlement, the university must also implement major reforms to address sexual harassment complaints, bolster its Title IX office, train student-athletes and university employees on giving and receiving consent before medical treatment, prevent retaliation, and provide support to current and former student-athletes who were sexually harassed by the athletic trainer.

The university said it already has restructured its Title IX office, added Title IX experts on gender equity, and launched a new chaperone policy that will give students and staff the right to request a third party be present for any type of sports medicine treatment.

San Jose State said it looked forward to partnering with the Department of Justice to build a stronger Title IX program.

“The health and safety of our campus community remains our top priority,” the university said. “We will continue to learn from the past so we never repeat it.”