MTA facilities across the city are still relying on ancient, punchcard timekeeping clocks to track worker hours, leaving the door open to potential overtime abuse, the agency’s inspector general said Thursday.

IG Carolyn Pokorny toured both the sprawling Coney Island Rail Yard and the Michael J. Quill Bus Depot in Midtown as part of her push for biometric timekeeping systems — like the fingerprint scanner taken out of commission by a saboteur before it was even operational, as first reported by The Post.

“I observed that many of the hundreds of employees who work at these facilities still use an outdated punchcard system with no verification mechanism, the very type of timekeeping approach that is most vulnerable to misuse,” said Pokorny.

She said that while most MTA employees are “hardworking and honest,” more modern measures are needed to discourage those who would cheat the system.

“Punchcard timekeeping clocks with no identity verification mechanism belong in the Transit Museum, not a modern railyard,” said Pokorny. “This is a failure of the management system, and taxpayers and riders deserve more.”

Gov. Andrew Cuomo, who appointed Pokorny and runs the MTA, had a similar message Thursday as he warned the still-unidentified saboteur that New Yorkers won’t tolerate scammers lining their pockets with taxpayer funds.

The review comes amid a widespread internal probe at the MTA, also led by Pokorny, into alleged overtime abuse at the agency, and particularly the Long Island Rail Road.

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