The NCAA has charged Boise State with a lack of institutional control following an alleged major violation in women's tennis and secondary violations in four sports, including football.
The school released its official response to the allegations Monday evening and will go before the NCAA's Committee on Infractions June 10. A final report and penalties will be issued several months after that meeting.
"We are deeply committed to following all NCAA rules and to ensuring that our athletic department works diligently so that our procedures reflect the highest standard," Boise State president Bob Kustra said in a statement. "I am disappointed that we face these allegations. It is unacceptable, and the athletic department staff understand and agree with my position."
The university has made fixes, done its own internal investigation and hired a new compliance officer, Kustra said.
The secondary violations in football involved impermissible housing, transportation and/or meals to prospective student-athletes from 2005 to 2009.
In all, the NCAA found the total value of impermissible benefits through five years was $4,934 for all of the housing, transportation and meals provided to 63 incoming student-athletes. All services ranged from $2.34 to a maximum of $417.55 and have been reimbursed by the student-athletes.
"We pride ourselves on doing things the right way at Boise State. As soon as we became aware that these inadvertent infractions were not in accordance with NCAA rules, we acted swiftly and without hesitation," football coach Chris Petersen said in a statement released by the school.
"The university, our staff and the involved student-athletes worked together with the NCAA to resolve the situation, including reimbursement of the benefits received, and that money was donated to a local charity," Petersen said.
Boise State began its investigation into potential violations in 2009. The school and NCAA agreed to penalties a year later for the sports that broke the rules: football, men's and women's tennis, and men's and women's track and field.
But later that year, Boise State self-reported a major violation in women's tennis, in which one tennis player was allowed to compete before being officially enrolled.
That led the NCAA to take the secondary violations and major violation and lump them into one case, slapping the more serious "lack of institutional control" charge on top of the existing violations.
"Complying with NCAA rules is fundamental to who we are and how we do things at Boise State," athletic director Gene Bleymaier said in a statement. "We have addressed the issues and are working with the NCAA to bring this to a close."
Andrea Adelson covers college football for ESPN.com. Information from The Associated Press was used in this report.