ALBANY — Gov. Cuomo is the state’s top elected official, but he’s far from being the highest paid state worker.

A whopping 3,568 state employees earned more in 2017 than the $179,000 salary paid to Cuomo, according to data the Empire Center for Public Policy released Thursday. The figure was up from 2016, when 2,928 workers earned more than Cuomo.

New York’s highest employee in 2017 was Carlos Pato, dean of the College of Medicine at SUNY Downstate Medical Center, who earned $746,626, the center said.

“SUNY Downstate is a teaching hospital in which many of our doctors, like Dr. Pato, have clinical practices,” a SUNY Downstate spokesman said in a statement. “Earnings from clinical practice are included in the overall annual compensation.”

According to the center, the 100 highest-paid state government employees all worked for either the State University of New York or the City University of New York.

Among them were two SUNY football coaches: Stony Brook’s Charles Priore at $418,219 and Buffalo’s Lance Leipold at $413,992. CUNY Chancellor James Milliken, who is retiring at the end of the current academic year, got a 37% pay hike to $670,000 in 2017, according to the center.

CUNY spokesman Frank Sobrino, however, denied that Milliken’s compensation increased.

Sobrino said a portion of Milliken’s salary had previously been funded from “interest income” from investments. In 2017, as part of a package of budgetary and ethics reforms, the school began paying his entire salary from the state tax levy, which makes it appear that he got a raise.

“There were no raises,” Sobrino said. “CUNY’s trustees passed a sweeping series of reforms to create greater transparency and accountability in response to concerns raised by the state inspector general. All executive compensation is now paid through tax-levy sources.”

Another three SUNY and CUNY administrators also received annual salary increases of more than $100,000, according to the Empire Center.

Getting big increases were SUNY Downstate Medical Center CFO Thomas Gray, whose base pay jumped 90% to $475,000, CUNY Graduate School of Public Health Dean Ayman El-Mohandes, whose base pay jumped 57% to $415,000, and Baruch College President Mitchell Wallerstein, whose base pay increased 33% to $400,000.

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