Labor leaders on Wednesday questioned the Metropolitan Transportation Authority’s new internal watchdog about her tactics in targeting employee time and attendance issues, including alleged overtime abuse.

The showdown came at a meeting of the MTA Board in Manhattan, where Carolyn Pokorny, the new MTA inspector general, discussed some of her efforts to weed out “waste, fraud, abuse and deficiencies” — including what she has said is an antiquated and ineffective system of monitoring employee hours worked at some facilities.

It was in the course of pushing for a modernization of that system that Pokorny said she discovered the “apparent sabotage” of two employee time clocks — one at an LIRR employee facility in Jamaica and another at a subway workers facility in Brooklyn. In that incident, Pokorny said her office’s investigators made the “educated assumption” that the face of the clock had been “smashed” by a worker’s elbow.

In questioning her characterization of the Brooklyn incident as sabotage, MTA Board member Norman Brown, who represents union workers, noted that the damaged time clock never stopped functioning.

“You haven’t really, in my mind, precluded that it could have been an accident, and entirely unrelated to sabotage,” said Brown, who raised concerns about her investigations contributing to the public’s distrust of MTA workers. “To characterize something as sabotage that you do not know is sabotage is sort of throwing gasoline on the fire.”

Pokorny said her investigators were able to narrow down when the damage occurred “within a few hours period” on June 7 because workers who were interviewed said they saw the time clock intact earlier that day. She said if the time clock was broken by accident, she would “question why whoever broke it wouldn’t have come forward.”

Pokorny defended her public handling of the incidents, saying it was important to get the word out about them, both to find witnesses with information, and to discourage similar incidents.

Gov. Andrew M. Cuomo last month picked Pokorny, a former federal prosecutor, to fill the office of MTA Inspector General amid growing concerns about potential overtime fraud at the authority. The concerns stemmed from an April report by the Empire Center for Public Policy, a conservative think tank, that revealed 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.

“My quarrel’s not with the workers, who I have thoroughly enjoyed meeting. I think they are honest. I think they work very hard and take great pride in their work,” Pokorny said. “We understand that overtime can be inevitable in getting the job done. That is not my focus. My office’s focus is on waste, fraud, abuse and making sure there are management systems in place, both to prevent fraud and give the public confidence that the overtime is necessary.”

The Queens District Attorney and U.S. Attorney’s Office for the Southern District are also looking into potential overtime abuse at the MTA. And MTA chairman Patrick Foye confirmed Wednesday that the MTA has retained attorney Carrie Cohen, another former federal prosecutor, to conduct a 60-day review of excessive overtime at the agency.

MTA Board member Vincent Tessitore Jr., who represents LIRR union workers, said the increased scrutiny is “weighing on our workers.”

Foye also defended LIRR president Phillip Eng’s decision to offer some union workers overtime pay in place of them taking state-permitted time off to vote in Tuesday’s elections. MTA officials said Eng encouraged employees to vote before or after their shifts, so that the railroad could have adequate staffing to serve riders.

“The right to vote is an incredibly important part of being an American and an incredibly important part of our democracy. I think Phil was focused on allowing every one of our workers . . . to be able to vote,” while also maintaining service, Foye said. “That was done effectively. I think the decision that Phil and the management team made was appropriate.”

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