MTA Chairman Pat Foye has ordered a crackdown on overtime abuse at the Long Island Rail Road — after new data showed workers are raking in massive paychecks by logging a staggering number of extra hours, sources told The Post Thursday.

“The MTA is going to aggressively look for creative ways to control overtime and address instances of overtime abuse,” a source said.

After the Empire Center’s SeeThroughNY noted this week that the LIRR shelled out $224.6 million for overtime in 2018 — up nearly $50 million from the previous year and more than $115 million since 2013 — it sounded alarms at the highest levels of the MTA’s management.

One worker, recently retired Chief Measurement Operator Thomas Caputo, raked in $344,147 in overtime last year — likely helping him secure a pension of $162,000 a year.

Foye’s probe will also examine possible safety and discrimination concerns related to the payment.

“The workers who get the most overtime are largely senior and not a diverse group,” the source noted.

The investigations come as negotiations over the LIRR workers’ cushy union contract are set to begin again.

Gov. Andrew Cuomo, who controls the MTA, helped renegotiate the deal in 2014, averting a looming strike.

That contract was renewed in 2016 with minimal changes, delaying any talks of serious reforms until last week, when that agreement expired, sources say.

In 2014, Cuomo was happy to accept praise for stepping in to help hash out the contract over a seafood lunch in Midtown, with a subsequent MTA press release celebrating his role in the deal.

“The agreement we have reached today is fair to all parties,” Cuomo was quoted as boasting in the release.

But when asked on Thursday how he would ensure the next contract curbed overtime costs, Cuomo claimed he had no power to slam the brakes on the off-the-rails spending in a new deal.

“The MTA negotiates directly with their union,” said a spokesman for Cuomo. “However, the governor has made it clear that the MTA must fundamentally change the way it does business, and that includes reining in spending that has led to its dire financial situation.”

In the 2014 contract, LIRR brass were seeking reforms to curtail payroll and overtime costs, which could have thwarted Caputo from logging a jaw-dropping 3,864 overtime hours last year.

Among them: scrapping the system that gives people with the most seniority first dibs on overtime and instead equalizing it among all employees based on attendance and overtime already worked, according to a federal report into the contract dispute.

Other proposed measures included changing some double-time payments to time-and-a-half and eliminating extra pay given to conductors when they work on both a passenger and freight train in the same shift.

None of the reforms was made, according to an MTA source.