Nine hundred state employees made more than Gov. David Paterson’s $179,000 salary in 2009, according to a report by the Empire Center for Public Policy, a conservative think tank.

The center reviewed payroll records of 298,247 New Yorkers that were employed in any state government branch in 2009.

The Empire Center posted last year’s base pay and total pay of all state employees on its Web site, SeeThroughNY.net, along with over one million county and city employees.

A pair of State University of New York officials topped the list. Dr. Stephen Onesti, chairman of the neurosurgery department at the SUNY-run Downstate Medical Center in Brooklyn, earned $958,047 last year, while Alain Kaloyeros, vice president and chief administrative officer of the nanoscience program at the University at Albany, earned $734,353.

Gannett’s Albany Bureau reported in February that the number of six-figure salaries on the public rolls in 2009 grew to 23,685 workers, up 16 percent from 2008. It was the largest total in state history and four times as high as it was in 2000, when 5,800 state workers made $100,000 or more.

SUNY defended the high salaries.

“The investment the state makes is returned many times over as State University of New York physicians and researchers attract millions of dollars to the communities they serve each and every year,” said SUNY spokesman David Henahan.

The report Wednesday revealed many employees earned large amounts of overtime and extra pay – sometimes hundreds of thousands of dollars worth. Mercy Mathew, a nurse at the Bedford Hills Correctional Facility in Westchester County, earned $171,814 on top of a base salary of $55,716.

“There were a lot of very high overtime numbers,” said Lise Bang-Jensen, senior policy analyst for the Empire Center. “We suggest that either overtime is out of control, or maybe they should be hiring more employees for certain jobs.”

In the state Legislature, the top eight earners all worked for the Senate. Shelley Mayer, chief counsel to the Senate Democrats, took home $181,757 in 2009, topping the list. Dean Fuleihan, Assembly Ways and Means Committee secretary, earned the most in the Assembly with $157,829.

Judge Lawrence Marks, administrative director of the Office of Court Administration and a Court of Claims judge, brought in the most among workers in the judicial branch. He took in $181,496 in 2009.

Of the top 50 earners in the executive branch, 39 worked in the state Office of Mental Health. All 39 were either psychiatrists or physicians, said Jill Daniels, spokesperson for the department.

“OMH provides inpatient and outpatient mental health services and in order to do that, we need to employ physicians and psychiatrists,” Daniels said. “And in order to hire them, we have to pay them.”

“There is a perception that public employees are underpaid,” Bang-Jensen said. “By putting these salaries online, New Yorkers can decide for themselves.”

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