The Chronicle, a Washington-based publication focusing on education, surveyed total compensation -- defined as salary and benefits -- for top executives at 185 public universities..
Gee is the only public university president to have earned more than $1 million last year. By contrast, The Chronicle reported in November that 23 presidents of the nation's top private universities took home more than $1 million in 2008, the most recent year surveyed.
In a statement, Gee said leading a public university is "a calling" adding that he feels an "unparalleled sense of urgency to fulfill the public trust."
"I am fully determined to make good on the University's great promise," he said. "We have a limitless capacity to do good in the world, and I will tell you that my eye never leaves the ball."
The Chronicle said Gee is one of "a growing number" of presidents that have given money back to their institutions, saying he donated $320,850 to help endow a scholarship fund.
Meanwhile, the survey found that compensation for public university executives overall increased at a much smaller rate in 2009 than in recent years. The median total compensation for chief executives last year was $436,111, up 2.3% from 2008. After adjusting for inflation, however, compensation rose 1.1%.
That compares with total compensation rising between 7.6% and 18.9% each year since 2005.
But as the economy soured and many public universities were forced to hike tuition and eliminate courses, the issue of executive compensation became a sore spot for many schools, said Jeffrey Selingo, editor of The Chronicle.
"Steadily rising pay packages of public university chiefs riled parents, students and politicians, especially as tuition increases also had been hefty from year to year," Selingo said in a statement.
The survey also showed that base salaries stopped growing last year for more than one-third of the public university heads, while 10% of them experienced a decline in total compensation.
The Chronicle also surveyed compensation at 64 community colleges nationwide and identified Eduardo Padrón, president of Miami Dade College, as the highest paid.
Padrón's pay package totaled nearly $550,000 last year. He was followed by Michael McCall, president of the Kentucky Community College and Technical College System, at roughly $532,000.
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