The presidents of Columbia University and the University of Pennsylvania both earned more than $3 million in 2013, topping a new national survey of compensation at hundreds of private higher education institutions.

Lee C. Bollinger’s total earnings from Columbia were $4.6 million, the Chronicle of Higher Education reported. That was the highest presidential compensation in the country. Bollinger’s base pay at the Ivy League school in New York that year was $1.2 million. He also received deferred compensation and bonuses.

Amy Gutmann’s total earnings as president of U-Penn. were $3.1 million, with base pay of $1.2 million plus bonuses and other compensation. That made her package second-highest in the country.

The 2012 survey showed Bollinger earned $3.4 million and Gutmann $2.5 million, ranking them third and fourth, respectively, that year in compensation.

In all, the Chronicle found, 32 chief executives among 558 analyzed nationwide earned more than $1 million in 2013. That was down slightly from the 2012 total of 36. The Chronicle relied on data from U.S. tax filings for its survey, which was published Sunday evening.

Presidential salaries are often controversial. Trustees say they must pay top dollar to get the best executives for highly demanding positions that require expertise in academics, fund-raising and operations of huge research and teaching enterprises. Pay often is higher for institutions that are seeking to climb in prestige.

High Point University President Nido Qubein earned $2.9 million in 2013, ranking third for his compensation from a North Carolina liberal arts school that has drawn national attention for huge investments in campus amenities. Harvard University President Drew Gilpin Faust earned about $930,000, ranking 42nd.

Critics say that the money is over the top at a time when many families are scrimping and taking out loans to afford charges for tuition, housing, food and other expenses that can total more than $60,000 a year at private institutions.

Republican presidential candidate Donald Trump was asked about college affordability in New Hampshire last week. “These colleges, they’re going through the roof,” he said. “Why are they going up so much?”

Among other reasons, Trump pointed to executive pay. “You look at the salaries paid to the heads of colleges, it’s like they’re running a business — a real business, a big business. And we have to stop, we have to stop that from happening.”

Jonathan D. Schiller, chair of Columbia’s Board of Trustees, defended Bollinger’s compensation.

“Under his leadership, we see Columbia is performing at a level and achieving a standing it has not enjoyed in many years, solidifying its place at the top rank of the world’s great universities,” Schiller said in a statement. “We’ve seen this in the prudent fiscal management of the institution, the historic success at fundraising and among top endowment returns in peer group, and academic leadership across our schools and disciplines.”

David L. Cohen, chair of the Board of Trustees at U-Penn., lavished similar praise on Gutmann.

“We believe she is the best university president in the country, and being No. 2 in the Chronicle rankings is consistent with that positioning,” Cohen told the Chronicle. “If you’re going to recruit and retain the type of talent that you need to run a university of this complexity and to continue to advance this university’s reputation and the quality of its product, you have to fairly compensate individuals for doing that job.”

Among university leaders in the nation’s capital, George Washington University President Steven Knapp is the highest paid. He received $1.1 million in 2013, the survey found. Sidney A. Ribeau received about that much as well, a reflection of his severance package as he abruptly retired from the presidency of Howard University in 2013. Ribeau’s total compensation was $1.06 million, including base pay of $644,000.

No other D.C. university leader earned more than $1 million in 2013. American University President Cornelius M. “Neil” Kerwin earned $935,000 in total compensation and Georgetown University President John J. DeGioia $851,000.

In Maryland, Johns Hopkins University President Ronald J. Daniels earned $1.6 million in total compensation. In Virginia, the highest-paid private university leader was Jerry Falwell Jr. As president of Liberty University in Lynchburg, his compensation was $900,000.

  1. Lee C. Bollinger, Columbia University — $4.6 million
  2. Amy Gutmann, University of Pennsylvania — $3.1 million
  3. Nido Qubein, High Point University — $2.9 million
  4. Richard M. Joel, Yeshiva University — $2.5 million
  5. Nicholas S. Zeppos, Vanderbilt University — $2.1 million
  6. Scott S. Cowen, Tulane University — $1.634 million
  7. Ronald J. Daniels, Johns Hopkins University — $1.629 million
  8. Marc Tessier-Lavigne, Rockefeller University — $1.46 million
  9. John E. Sexton, New York University — $1.45 million
  10. C.L. Max Nikias, University of Southern California — $1.42 million