The MTA will hire an outside consultant to review its payroll systems amid outrage over extraordinary overtime bills filed by some employees at the Long Island Rail Road.

MTA chairman Pat Foye on Wednesday announced the transit agency’s board had signed off on the 60-day outside examination after a raucous two-hour debate that occurred mostly behind closed doors.

“I think it’s clear that the timekeeping and attendance processes and systems vary across the agency, they vary within the agency,” Foye told reporters after the meeting. “These are serious issues.”

But, he added, the consultant would not specifically probe overtime at the state agency.

MTA board member Larry Schwartz — a close ally of Gov. Andrew Cuomo’s — had originally pressed for the MTA to hire a former prosecutor to examine overtime at the system, which sparked fierce protests from the agency’s labor unions.

“I do not believe that there is a large amount of systematic, overtime fraud. I think there are abuses,” Foye said, discounting the idea that rampant fraud was pushing the MTA’s overtime bill skyward.

“If you think of the MTA as a city of 70,000 people,” he added, “like any city of 70,000 people, you’re going to have a lot of fine, upstanding people and you’re going to have a very small minority of people who sadly cheat.”

Government watchdogs and transit advocates have put new pressure on the MTA to tackle its labor costs after fiscal watchdog group the Empire Center revealed it spent $1.3 billion on overtime in 2018.

The Post highlighted the eye-popping overtime hours logged by some LIRR employees last year — including those who billed for more than 3,000 hours in extra work, leading to demands for reforms and investigations into labor practices at the agency.

Foye previously announced in May that the MTA’s inspector general would probe its overtime in work rule practices and he instructed the MTA’s subway and commuter rail division chiefs to mount their own reviews.

The Queens District Attorney’s Office and Manhattan federal prosecutors are also eyeing the giant transit agency’s labor costs — and the LIRR’s antiquated use of handwritten time sheets.

© 2018 New York Post