A suspected saboteur cut a cable on a fingerprint scanning machine installed at one of the Long Island Rail Road’s busiest stations to cut down on rampant agency overtime abuse — spurring a thorough investigation of the Queens transit hub by MTA investigators Wednesday.

When workers came to install the biometric timekeeping system in Jamaica Station on Tuesday, it was found with one of its cables clipped, officials told The Post.

The apparent sabotage triggered an investigation by the MTA’s Police Department and Inspector General’s Office, which on Wednesday afternoon descended on the station, searching for clues — and a culprit.

“The wire didn’t cut itself,” said newly minted IG Carolyn Pokorny. “It’s obviously disturbing for anyone to be sabotaging the system that was meant to ensure attendance is timely, accurate and correct.”

Investigators didn’t immediately identify a suspected saboteur, and several MTA employees have keys to the room that houses the high-tech machine, which is meant to keep workers honest by forcing them to clock in and out with their fingerprints, sources said.

The moves come amid a sweeping internal probe, spearheaded by Pokorny, into long-running overtime abuse at the MTA and, in particular, the LIRR.

The Empire Center, a fiscal watchdog group, in April released a report detailing borderline-impossible levels of OT being racked up by some MTA honchos, launching a series of Post exposés into some of the biggest beneficiaries.

The overtime bills allowed the LIRR’s top earner, chief measurement operator Thomas Caputo, to take home a $461,646 paycheck in 2018 — fattening his pension just before his retirement.

Another LIRR employee, track worker Marco Pazmino, clocked 4,157 hours in overtime alone, which allowed him to quintuple his base salary of $55,000 and take home a total of $311,162 in 2018.

MTA chairman Pat Foye admitted the extraordinary time sheets — if the hours were actually worked — likely constituted a risk to public safety due to fatigue and exhaustion as he ordered an authority-wide review of labor practices in May.