NEW YORK (CNNMoney) -- Some private colleges are paying their top executives millions of dollars, at the same time they're hiking tuition prices for students.
Vanderbilt University paid its chancellor, Nicholas Zeppos, $1.9 million in 2009, according to the school's most recent tax filings -- enough for up to 43 students to attend Vanderbilt at current prices. His total pay includes a base salary of $673,002, as well as bonus and other compensation.
That same year, Vanderbilt's tuition jumped 4.3%. Since then, the college has hiked tuition more than 3% annually, and now totals $41,332, according to the university.
His overall pay was actually 21.5% lower than it was the previous year, according to the school. Even so, Zeppos' 2009 base was almost four times the average professor's salary of $179,600, the college confirmed.
Zeppos "deserves the compensation he receives," said Mark Dalton, chairman of the college's Board of Trust, in a statement.
"We know that Nick is a highly attractive candidate for other top universities seeking new, vibrant leadership," Dalton said. "We cannot allow another university to recruit him away from Vanderbilt on the basis of compensation or other factors."
Quinnipiac University, located in Hamden, Conn., is in the same boat. Its president, John Lahey, made $1.2 million in 2009, including base pay of $760,706, according to tax documents. Meanwhile, the college raised tuition and fees nearly 5% that year, and more than 5% each year after. Students now pay $36,130 a year to attend.
Emory University, in Atlanta, and Houston-based Rice University also paid their presidents more than $1 million in 2009 while raising tuition nearly 5%. Both schools have also hiked tuition during the past two years.
As student loan debt continues to grow and students storm campuses across the country to protest the surging cost of tuition, college presidents' big paychecks are adding fuel to the fire, said Sara Hebel, a senior editor at the Chronicle of Higher Education, which recently published its annual survey of CEO compensation among private colleges.
"At a time when the national conversation is focused on widening income gaps between the wealthiest individuals and everyone else, it is not a surprise that college presidents who earn some of the highest salaries have been targeted by students who face rising tuition," said Hebel.
Of the 519 private colleges with budgets over $50 million that the Chronicle surveyed, 36 presidents earned more than $1 million in 2009. That's up slightly from the 33 presidents who topped $1 million in earnings during the previous year. The Chronicle report, which is based on the most recent tax documents available, looks at compensation including base salary, bonuses and the value of benefits.
Some of the presidents got million-dollar pay because they retired from their schools that year -- and their packages were bulked up with deferred compensation, retirement benefits, sabbatical leave compensation and other one-time payments.
The median total compensation of the 519 presidents at colleges surveyed by the Chronicle was $385,909. That's a 2.2% increase from 2008. The median base salary was $294,489, a 2.8% bump up from the prior year.
Tuition has been increasing at an even faster rate. Private colleges raised tuition by an average of 4.3% for the 2009 school year, according to the National Association of Independent Colleges and Universities. And the hikes have been continuing. Private colleges increased tuition and fees by 4.5% for 2010, and 4.6% for the current school year.
While stated tuition and fees are higher, the actual amount students are paying at some colleges may be decreasing. Some schools are ramping up financial aid at the same time, making the "sticker price" misleading.
For example, while the University of Pennsylvania's published tuition and fees have surged 37% over the past seven years, the average net cost (including financial aid) for students aided by the college has actually decreased about 4%. Only the wealthiest families (those earning annual income of more than $200,000) pay the full sticker price, the university said.
That said, the president of University of Pennsylvania, Amy Gutmann, still earned a handsome base salary of nearly $900,000 in 2009, the main chunk of her $1.3 million in total compensation, according to the university's tax filings.
And Hebel said that while presidential salaries hold symbolic importance, especially at a time when college is becoming increasingly unaffordable for the average family, the typical president's compensation package actually makes up only 0.4% of a college's budget.
Of course, there are bigger gaps at some schools. While inflated thanks to a one-time retirement payment in 2009, the $1.8 million in compensation given to the president of Beckley, West Virginia-based Mountain State University accounted for 3.5% of the school's entire budget, according to Chronicle data. 
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