University at Buffalo President Satish K. Tripathi was the highest-paid president in the State University of New York system in 2012-13 and the 29th highest-paid public university chief executive in the country, according to a Chronicle of Higher Education analysis.

Tripathi made $681,139 in 2012-13, including $643,309 in base salary and $37,380 in retirement pay. His pay increased about 6 percent from the previous year, when he made $641,957.

Michael E. Cain, vice president for health sciences and dean of medicine at UB, was not far behind, earning $674,680 in total compensation in 2012-13.

Cain made more than the next-highest paid executive in SUNY, Samuel L. Stanley Jr., who earned $664,855 as president of the State University of New York at Stony Brook.

Trpaithi, Cain and Stanley all made more than Nancy L. Zimpher, who as chancellor oversees the entire SUNY system. Zimpher earned $621,200.

Those are the latest figures available.

The median compensation for chief executives at public colleges in 2012-13 was $478,896, up five percent from $404,496 in 2011-12, according to the Chronicle’s annual analysis.

The newspaper analyzed the pay of 256 leaders at 227 public colleges and systems, including all public doctoral universities in the U.S.

Nine chief executives made at least $1 million in 2012-13, including top earner E. Gordon Gee at Ohio State University.

Gee’s compensation was $6,057,615, more than 40 percent of which came in the form of a deferred compensation payout. His base salary was about $850,000.

Gee resigned from Ohio State in 2013 and is now president at West Virginia University.

UB’s third-highest paid employee was Animesha A. Sinha, head of the dermatology department, at $475,760. Charles F. Zukoski, provost and executive vice president for academic affairs, was next at $432,000.

The Chronicle calculated that Tripathi’s base pay was 4.8 times the average salary of full professors at UB and accounted for 0.07 percent of UB’s total expenses.