More than 2,500 Port Authority employees pulled down salaries exceeding $100,000 last year – including a police sergeant who took home $250,000, a watchdog report released Tuesday shows.

The payroll at the Port Authority grew by more than $15 million to $664.7 million from 2008 to 2009, thanks in part to eye-popping paychecks for some employees, according to the report.

The Empire Center for Public Policy, part of the fiscally conservative Manhattan Institute, found 54 people made more than $200,000 last year, much of it overtime.

A little more than a third of the agency’s 7,499 employees made more than $100,000.

The top salary on the PA’s payroll went to Executive Director Christopher Ward – more than $304,000. Former Deputy Executive Director Susan Bass Levin made $290,862.

The study zeroed in on police overtime as a problem and a few cops in particular.

One police sergeant made more than $250,000 last year, including overtime, more than doubling his base pay and outearning all but the two highest-paid PA execs. One cop pulled down $207,265, more than doubling his base pay of $99,923, while another broke the $200,000 barrier, with more than $111,000 in overtime on top of his $89,647 salary.

Port Authority spokesman John Kelly defended the agency’s overtime spending, calling it “something that we watch closely.”

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