Gora's pay for that year included some $500,000 in deferred compensation and incentives on top of her base salary of about $430,000. Much of that came from a retention incentive for staying at Ball State for five years, from 2007 to 2011, university spokesman Tony Proudfoot said.
Gora has averaged about $436,000 in pay over her nine years as president, Proudfoot said.
Hollis Hughes Jr., president of the Ball State Board of Trustees, called Gora's pay an anomaly that reflected "unusual circumstances."
"We certainly don't overpay our president," Hughes told The Indianapolis Star.
In 2011, about 36 percent of college and university presidents had deferred-compensation agreements, said Terry Hartle, senior vice president of the American Council on Education.
He said he wasn't surprised by Gora's pay package for leading the Muncie campus of about 18,000 students.
"If I were them, I would very much want to ensure that Jo Ann stays at Ball State instead of leaving," Hartle said. "Ball State is a very different institution than it was when she arrived. I think it's a far stronger place with a much bigger national profile. ... I completely believe she is worth it."
David Pearson, an associate professor of exercise science and chairman of Ball State's University Senate, also defended Gora's pay.
"If people would see the university as the major corporation that it is, she is vastly underpaid in comparison with other similar CEOs," Pearson told The Star Press. "Why don't you report how many million dollars she has raised in the face of cuts from Indy to help BSU?"
The Chronicle's survey listed Indiana University President Michael McRobbie with $653,258 in total compensation, putting him 32nd among the public college leaders. Then-Purdue University President France Cordova ranked 64th with $550,250.
Hughes said the Ball State trustees have wanted to keep Gora because "she started some pretty ambitious things."
"She's re-imagined the university, if you will, over the years, and we wanted to make sure the architect who worked with the board on this kind of plan was still with us," Hughes said.