The MTA Inspector General posted a picture on social media of the clock that employees use to clock in and out.
It is located at the 38th Street train yard in Brooklyn.
Earlier in the week, a wire was cut on a biometric clock at the LIRR Jamaica station.
Union leaders had called on the MTA to fully investigate that incident before labeling it as sabotage.
The alleged vandalism comes as the MTA tries to crack down on employee overtime abuse, after a new report found transit workers made about $400 million in overtime pay last year.
Anyone with information about the incidents is asked to call the confidential MTA IG tip line: 1-800-682-4448.
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