Gov. Cuomo on Sunday voiced his harshest comments yet about workers at the MTA’s Long Island Rail Road who claimed they worked an outrageous number of hours to jack up their paychecks.

​”​This is about stealing. This is about fraud. This is about people saying they work and charging the taxpayers when they didn’t work. It’s stealing. It’s criminal​,” the governor said during a news conference at his midtown Manhattan office. “​So this has nothing to do with overtime. It has to do with theft and fraud, and that’s criminal.​”​

​Cuomo said the Metropolitan Transportation Authority approved overtime hours for workers but “we never authorized fraud and theft and criminality.”

He went on to question why MTA management ​did not step in and put an end to the practice of billing for excessive overtime costs.

​”​This is not a new issue for the MTA. They have been criticized for years on lack of an effective time and attendance system. Why didn’t they change it? Why didn’t they fix it? There’s no excuse in my opinion​,” Cuomo said, adding he agreed with MTA chairman Patrick Foye for the need to appoint an independent investigator.

​”Find out, A, to the extent they can, how widespread the fraud, or possible fraud, is, and B, explain to the MTA what management system has failed that has allowed this to go on and didn’t catch it​,” he said.

John Samuelsen, the president of the Transport Workers Union, pushed back at Cuomo’s comments.

“Of course, I support and honest day’s pay for an honest day’s work. There is no systemic abuse or criminality [in overtime],” he said, adding that it’s a “smokescreen about a problem that doesn’t exist.”

Instead, Samuelsen called for an investigation into the MTA’s hiring of outside consultants, claiming that $2.1 billion has been wasted on them.

“They flushed money down the toilet on politically connected outside consults … who are feeding on the trough of public money,” he said.

The governor also told MTA officials to stop making excuses about the Subway Action Plan contributing to soaring overtime costs, saying there are “no excuses left.”

“The MTA has gotten all the support that they’ve requested. They’ve increased fares, we’re planning future toll increases, we’ve passed legislation that gave them powers they’ve never had before,” he said. “So my position now is, it’s time for the MTA to perform.”

“They said they needed more money, more money, more money. They raised fares. Now we’re saying we need more service, more service, more service. It’s not an issue of overtime,” Cuomo said.

Those costs were already factored into the $836 million Subway Action Plan, which Cuomo said simply calls for the MTA to do its job: “Clean the stations, clean the cars, fix the tracks, fix the signals.”

​Foye has called for cracking down on soaring overtime costs at the transportation agency in 2018 after The Post reported on how some employees put in for eyebrow-raising hours.

Recently retired LIRR employee Thomas Caputo claimed he worked an additional 3,864 hours to rake in $344,147 in overtime pay in 2018 for a grand paycheck of $461,646, according to the Empire Center.

Another LIRR worker, Marco Pazmino, put in for 4,157 overtime hours, quadrupling his $55,000 yearly salary.