(CBS) The University of Illinois has fired athletic director Mike Thomas, the school announced Monday morning, in conjunction with the release of a final report into allegations of mistreatment in the football and women’s basketball programs.

Thomas had been under heavy criticism during a rocky tenure that included a disastrous hiring of football coach Tim Beckman and allegations of player mistreatment in football, women’s basketball and women’s soccer. The report didn’t find wrongdoing by Thomas, but the school believed change was needed.

Thomas had been at the school since August 2011.

“Mike Thomas has done a good job of leading through recent challenges,” interim chancellor Barbara Wilson said in a statement. “Decisions such as these are always difficult, but we have to focus on the best interests of our student-athletes. I believe this decision allows everyone to move forward.”

Beckman was fired in late August, just a week before the start of the season, after an the preliminary results of the investigation found that Beckman’s actions didn’t “reflect our values or our commitment to the welfare of our student-athletes,” Thomas said at the time.

Now, that investigation by Chicago-based law firm Franczek Radelet has been completed, and Thomas himself is out as well. The full report is a scathing review of Beckman, finding that he “discouraged student-athletes from seeking assistance from sports medicine personnel.” The report also found that Beckman threatened to pull scholarships from players, which is against NCAA rules and acted as a force to push players to play through injuries.

“He also systematically sought to influence sports medicine staff decisions and push student-athletes to perform despite medical concerns,” the report wrote of Beckman. “Whether intentional or not, his statements and conduct also appear to have deterred players from bringing medical concerns to the attention of athletic trainers and medical professionals and, when reported, to have encouraged them to return earlier than sports medicine staff may have otherwise decided.”

In addition to Beckman’s wrongdoings of scholarship mismanagement and pushing injured players to participate in the football program, the women’s basketball program led by coach Matt Bollant also came under heavy criticism after former players alleged the coaches bullied players, medically neglected them and created a racial divide, among other misdoings.

A former women’s soccer player also sued the university over the program’s handling of her concussions.

In the school’s press release, Thomas said he thought the reports showed he acted “appropriately and immediately” when issues of student welfare were brought to his attention but he relayed an understanding of why he’s out as the athletic director.

Here’s Thomas’ full statement:

“I understand the administration’s decision to turn the page and turn the focus of this organization back on the success and welfare of our student-athletes. The reports indicate that I acted appropriately and immediately whenever I learned of any issues related to the safety and well-being of our students. However, I understand the chancellor’s viewpoint that my continued presence may create an ongoing distraction for our students, coaches and staff, and I accept the situation.

I am honored to have served in this role for the past four years and I am proud of the accomplishments of our students during this time – on and off of the field. They have excelled in competition, in the classroom and in the community, and they exemplify the humility, dedication and work ethic that are hallmarks of this university.

My tenure has always been guided by the simple idea that my job is to do whatever is best for the University of Illinois.

It has been my privilege to be part of this storied program and this great university. I will always cherish my time at this institution and in this community.”

Since Thomas took over as athletic director in August 2011, the men’s basketball program has won one NCAA Tournament game in four seasons and hasn’t challenged for a conference title. The football program went 24-35 while Thomas was in charge.

Thomas hired Beckman in December 2011 and men’s basketball coach John Groce in March 2012.

Thomas’ annual pay was $568,178, the Associated Press reported. He’ll receive $2.5 million from the school after his departure, according to reports out of Champaign.

Senior associate athletic director Paul Kowalczyk has been named the interim athletic director.