The MTA’s new internal watchdog is investigating what she says is the apparent “sabotage” of a device used to record Long Island Rail Road employee attendance and timekeeping at Jamaica station, officials said Wednesday.

MTA Inspector General Carolyn Pokorny on Wednesday sent investigators from her office, assisted by MTA Police officers, to the facility where workers installing new biometric time clocks discovered an ethernet wire recently installed for use with the unit had been cut, a source with knowledge of the investigation said.

In a statement Wednesday, Pokorny called it “shocking and unacceptable to learn that one of these devices has been sabotaged.”

The MTA recently began installing the new time clocks at all employee facilities as part of its effort to address alarmingly high overtime rates among some employees, as uncovered in an April report by the nonprofit Empire Center for Public Policy. The report revealed that the MTA’s top earner in 2018, LIRR chief measurement officer Thomas Caputo, made $344,147 in overtime on top of his base salary of $117,499.

The Queens district attorney, the U.S. attorney for the Southern District and the MTA inspector general are also looking into potential overtime abuse at the authority.

The biometric devices require employees to scan their fingerprints to record when they report for work and when they leave for the day. MTA officials have expressed concern about the accuracy of the various other systems previously in place at the LIRR that record employee time and attendance, including paper forms and telephone check-ins.

“This office will have zero tolerance for any sabotaging of the equipment that is vital for ensuring the integrity of our timekeeping system,” Pokorny said. “I am directing our office to both work with the MTA Police to determine who performed this illegal act, and investigate whether this matter demands additional reforms and precautions across the LIRR system.”

Christopher Natale, general chairman of the Brotherhood of Railroad Signalmen Local 56, which represents the LIRR workers who installed the systems, said Pokorny’s office was “jumping to conclusions,” especially since the installation of the device was incomplete.

“It wasn’t a working wire,” said Natale, who called the accusation of sabotage “ludricrous.”

“That’s an allegation they made without talking to us,” said Natale, who supports the use of the biometric clocks. “Nobody’s opposed to it. We’re not here to keep secrets.”

But the source with knowledge of the investigation said a note left beside the cut cable addressed to “my fellow crazy coworkers” asked that they not “cut the cord again.”

The source said, upon finding the culprit, Pokorny could refer the matter to the LIRR for disciplinary measures, or, if appropriate, to prosecutors for criminal charges.

Since being confirmed by the State Senate last week, Pokorny — former special counsel in charge of public integrity for Gov. Andrew M. Cuomo — has hit the ground running. In addition to taking over the probe into overtime launched by her predecessor, Barry Kluger, on Monday Pokorny said her office was investigating the LIRR train derailments that shut down service to the South Fork during much of Memorial Day weekend.

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