For the past 15 years I served as president of San Diego State University. I sat in meetings and participated in votes about not just the academic life of the university but another huge aspect of university life: college sports. That experience leads me to recognize a few plain truths: College football is in a crisis; today’s system cannot fix itself. Indeed, no one on the inside of intercollegiate athletics can speak openly because too much is at stake. And taxpayers nationwide are harmed as a result.

The scrutiny of the media, Congress, the Justice Department and state attorneys general is warranted — and desperately needed — on the Bowl Championship Series. The BCS, the entity that controls college football’s four major bowls as well as its national championship game, has endless perverse incentives around its ESPN television contract, sponsorships, power and exclusivity.

National and state policymakers should care that college football is in crisis because taxpayers are on the hook. The vast majority of teams represent publicly funded institutions — from Ohio State and the University of Maryland to the Air Force Academy and Pittsburgh. Decisions made within the BCS system have a major effect on these schools.

Under current rules, college football’s postseason favors the “right” conferences and distributes revenue based on entitlement, not performance. For instance, in 2010 the Mountain West Conference, with the third-ranked team in the country, received approximately $10 million less than the Big East, which had no team ranked in the top 20. The BCS system siphons resources from schools in the “wrong” conferences, leaving taxpayers to make up large deficits from these schools’ athletic departments via state appropriations. College football should be about hard work, skill and determination, not about which conference one plays in.

But even if taxpayers’ concerns weren’t at issue, the mess that is college football is hurting student-athletes, fans and the schools themselves. Recent headlines (Arizona Republic: “BCS spending, gifts raise questions and criticism”; “College football season to start after scandal-marred summer”; Sports Illustrated: “Realignment’s musical chairs would leave several schools in the dust”) have shown a system corrupted by money, recruiting violations and upheavals in conference alignments.

Worse, the problems are spilling over from football to other sports. If you have read about Syracuse, Pittsburgh, Texas, Texas A&M, Oklahoma, Oklahoma State or any of the other schools planning or rumored to be considering switches from one conference to another — tumultuous changes revealed in just the past few weeks — then you know that football runs the risk of marring all college sports. That’s because when a football team switches conferences, all athletic teams at the school switch. In other words, with one decision many dominoes fall. March Madness? If “super conferences” are created and separate from the NCAA, the contest’s form will be jeopardized. Long-standing rivalries between two state institutions? Very possibly no more. Women’s basketball? No one’s asked for their opinion.

What’s going on here?

As in all situations of coercion, the victims are afraid to speak. University presidents by and large are not the villains here; the BCS forces good people to make bad choices. Many of us believe that the BCS is in violation of antitrust laws. But that is for the Justice Department and others to examine. The reality the past few years is that undefeated football teams (Auburn, Boise State, TCU and Utah) can’t play for the national championship, and thus lose prestige and needed financial rewards, because a cartel stands in the way. At minimum, this raises significant public policy questions. Even President Obama has noted the unfairness of the system.

Those who have watched this unfolding drama of musical chairs see its importance not only to the football team but to all sports at a school. We understand that our nation’s college sports teams are not facing a conference realignment problem but a systemic problem.

It is one thing to see that college football is a mess; it is another to understand why, what the panoply of consequences are and what can be done about it. Much hangs in the balance: student-athletes, taxpayer dollars, scholarship funds, and the integrity of the sport itself. The Justice Department and others cannot blow the whistle too soon. Fixing college football, and in particular its postseason, is the right thing to do for America’s game.

The writer retired in July as president of San Diego State University, a school that does not automatically qualify for BCS games. During his tenure, he served on the BCS Presidential Oversight Committee and was a member of the NCAA board of directors.