Three of the highest-compensated private college and university presidents in 2011 were at the helm of Massachusetts schools, according to a survey released Sunday by the Chronicle of Higher Education.
In 2011, the presidents of Northeastern University in Boston, Tufts University in Medford, and Amherst College all received hefty compensation packages worth more than a million and a half dollars. Each had his pay bolstered by big, one-time retirement benefits, a source of recent controversy at other schools.
The annual report, based on the tax filings of 500 private, nonprofit colleges and universities, provides a national perspective on academic compensation — a subject often fraught with emotion in an era of staggering tuitions and students burdened with loan debt.
The Chronicle of Higher Education survey, based on the most recently available data, found that in 2011, Northeastern University’s president, Joseph E. Aoun, was awarded $3.1 million in total compensation, more than every other college and university chief except the president of the University of Chicago, Robert J. Zimmer, who had total compensation of $3.4 million.
Henry Nasella, chairman of Northeastern University’s Board of Trustees, said in a statement that Aoun’s 2011 compensation included $2 million that was set aside for Aoun but will not be paid out until his time at the university ends.
“Through President Aoun’s leadership, Northeastern has achieved levels of excellence that were unimaginable when he was appointed in 2006,” Nasella said.
Fifth on the list was a former Tufts University president, Lawrence S. Bacow, who retired in the summer of 2011 after a decade at the school. His total compensation in 2011 was $2.2 million, the survey found.
Tufts spokeswoman Kimberly M. Thurler said in a statement that the figure included “a one-time, lump-sum payment of approximately $1.7 [million],” which included salary and benefits in lieu of an earned sabbatical, as well as accrued vacation.
A former Amherst College president, Anthony W. Marx, who left that job in June 2011, notched 11th place on the list, with $1.6 million in total compensation. Amherst spokesman Peter Rooney said in addition to that year’s $215,000 “regular compensation,” Marx received about $1.4 million in deferred compensation and unused sabbatical time after he left his post.
According to the survey, two other Massachusetts university presidents in 2011 received more than $1 million in total compensation, which includes take-home pay, benefits such as health care and housing, and money set to be paid out in later years.
Former Massachusetts Institute of Technology president Susan Hockfield, who left that job in mid-2012, came in 28th, with $1.2 million in total compensation for 2011.
Boston University president Robert A. Brown placed 14th on the list, with $1.4 million.
Representatives of some of the schools — BU among them — defended the compensation packages as being in line with the benefits the school reaped from the presidents’ leadership.
“He’s certainly well worth it,” BU spokesman Colin Riley said of Robert Brown.
And what of Massachusetts’ most famous private university?
Drew Gilpin Faust, the president of Harvard University, placed 54th on the list, with just under $900,000.
The survey found that nationwide in 2011 a total of 42 private college and university chief executives topped $1 million in total compensation.
It found the median total compensation was $410,523, a 3.2 percent increase over 2010.
The Chronicle of Higher Education survey examined the 500 private, nonprofit institutions of higher education with the largest endowments as reported to the US Department of Education. The Chronicle, a Washington, D.C.-based publication that covers colleges and universities, used data from Internal Revenue Service Form 990, which is submitted by most nonprofits and is public record, to calculate compensation.
The Chronicle notes, however, that some private, nonprofit universities, citing a religious exemption, do not file the form, and are thus not included.
How much college and university presidents are paid — during their tenure and in retirement — has, in recent years, became a point of controversy at various Massachusetts institutions.
More than 1,000 Brandeis University students, alumni, and other people with ties to the school signed a petition expressing anger last month after the Globe reported former president Jehuda Reinharz had received at least $1.2 million for part-time work since he stepped down as the school’s leader in 2010.
Reinharz and the school have defended the post-presidential pay as deserved, citing his accomplishments during his tenure.
Suffolk University became enmeshed in controversy in 2009 and 2010 and faced alumni and faculty furor about how much it paid then-president David J. Sargent, who received $1.5 million in total compensation in 2009.
Sargent stepped down in 2010.
Clarification: An earlier version of this story gave a different description of the compensation package of Northeastern President Joseph E. Aoun.