Nine months after the University of Virginia removed its president, prompting a storm of protest, and then reinstated her, the university still cannot go more than a few days or weeks without some new reminder of that spectacle, or persisting tensions between the president and the trustee who ousted her.

But the dispute long ago stopped being just about Virginia. Conflict over governing the university has become a proxy war in a much larger struggle over control of the nation’s public universities, with educational groups weighing in on opposing sides of the Virginia confrontation, and taking shots at each other.

Around the country, waning state support, rising tuition and the competitive threat of online education have raised fears about the future of public universities. Trustees and politicians in several states have increasingly flexed their muscles to influence university operations, leading to turf battles with presidents and chancellors who are largely used to having their way.

“In any sector that’s in the middle of stress and change, the relationships between C.E.O.’s and their boards gets more complicated, and these are very stressful times to be running a university,” said M. Peter McPherson, president of the Association of Public and Land-Grant Universities, who has held several high-level posts in business, government and academia, including president of Michigan State University and chairman of Dow Jones & Company.