For the second time in a week, a Metropolitan Transit Authority timekeeping clock has been damaged, officials said on Saturday, amid a probe into overtime pay at the LIRR and across the MTA.

MTA Inspector General Carolyn Pokorny, in a statement, said she was launching an investigation of what she called “an apparent act of vandalism” at the 38th Street Train Yard & Facility in Brooklyn.

Earlier this week, workers discovered a newly installed Ethernet wire had been cut at Jamaica station before the timekeeping devices could be set up. In Saturday’s incident, the front of the clock appeared to have been smashed.

“Riders and taxpayers deserve to have a modern system in place to effectively verify when workers arrive at the job, and clock out at the end of their shift,” she said.

“We will not be intimidated by illegal acts of sabotage that are only designed to undermine our efforts to ensure accountability across the MTA and protect taxpayer dollars from misuse,” the inspector general said.

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.

Gov. Andrew M. Cuomo on Thursday said taxpayers will not tolerate getting ripped off when it comes to possible overtime fraud, and he defended Pokorny for bringing “long overdue” accountability to the embattled transit authority.

John Samuelsen, international president of the Transport Workers Union, which represents MTA subway workers, said the timekeeping system being investigated by Pokorny is not used by transit laborers, but rather by MTA management. “So she better start looking for some angry, frustrated bosses,” he said.

The installation of modernized timekeeping and attendance systems for transit workers still have not begun, as the details need to be negotiated with the unions. Samuelsen said he doesn’t believe Pokorny realized that, but “increased the target on the backs” of union workers anyway.

“She’s probably doing it out of ignorance, and not on purpose,” he said. “No TWU official is condoning sabotage or criminality. But we also recognize that broad allegations that wrongfully expose workers to harm’s way are outrageously irresponsible.”

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