The Long Island Rail Road’s overtime costs, which already are more than $3 million over budget in 2019, have soared more than 50 percent over the last four years, despite the MTA repeatedly saying it would look to rein them in.

In May 2015, responding to concerns from board members about growing overtime costs, the Metropolitan Transportation Authority issued a special report concluding it needed to focus on overtime spending and “that efficiencies will be identified that will result in overtime savings.”

But overtime at the LIRR has climbed every year since, reaching $162 million last year — 51 percent more than in 2015. Through February of this year, overtime costs at the LIRR again were higher than in the first two months of last year, and at $12 million was $3.2 million over budget.

Heightened concerns about the railroad’s overtime spending followed an MTA payroll report issued last week by the nonprofit Empire Center for Public Policy that revealed the authority’s top earner in 2018 — LIRR chief measurement officer Thomas Caputo — took home $344,147 in overtime, on top of his $117,499 salary.

The report was released the same week the LIRR’s latest fare increase took effect, raising the cost of the average railroad ticket by about 4 percent.

In a statement Monday, MTA chairman Patrick Foye expressed concern about certain employers working extensive amounts of overtime, which he said could result in fatigue and dangerous consequences. Foye said he has asked LIRR president Phillip Eng to “look into this matter” and report back to the MTA Board.

“Someone who has worked hundreds of hours in a week should not be driving their personal car, let alone operating or working around railroad equipment,” Foye said. “These extended hours clearly could pose a safety risk to workers.”

MTA officials noted that federal law places restrictions on how many consecutive hours certain railroad employees, including locomotive engineers, can work.

The chairman of the State Senate Transportation Committee, Tim Kennedy (D-Buffalo), said he looks forward to reviewing the MTA’s plan to address what he called “excessive overtime” and is open to holding public hearings on the issue if necessary.

“I have continually raised concerns, both publicly and privately, about inflated salaries, bloated bureaucracy, and potential overtime fraud and abuse at the MTA,” said Kennedy, adding that he joins with Democratic lawmakers from Long Island in “working to hold the MTA accountable.”

The railroad has attributed much of the recent overtime to its work in advancing several capacity expansion projects underway, including the East Side Access effort to link the LIRR to Grand Central Terminal, and the construction of a second track between Farmingdale and Ronkonkoma, which was completed in September.

Several efforts included in Eng’s “LIRR Forward” service improvement initiative also have driven up overtime in recent months, according to the railroad. That includes increases in track tie replacements, in cleaning efforts, in repairs on the railroad’s 1980s-era “M3” trains, and in track geometry rail inspections — which were performed by Caputo, who since has retired.

LIRR documents show the largest category of overtime last year was “programmatic/routine maintenance,” which is defined as planned overtime for work “not resulting from extraordinary events.” The railroad has noted such work is typically performed “during hours that are deemed more practical in order to minimize service disruptions.”

Responding to the Empire Center report last week, MTA spokesman Maxwell Young pointed out that union work rules negotiated through collective bargaining “allow those with the most years on the job to get first pick at overtime opportunities.” He said the MTA is “absolutely committed to reducing spending” throughout its agencies.

MTA management’s increased scrutiny of overtime at the railroad comes amid a public rift with the head of the LIRR’s largest union, Anthony Simon, who has said Eng’s administration has failed to give its labor force adequate resources while spending millions on management salaries and consultant contracts. The railroad employs about one manager  or supervisor for every four hourly operational workers, according to MTA budget documents.

Simon again blasted the MTA’s handling of the overtime controversy as “disgraceful,” and said it comes as its unions are working under an expired contract and have not been invited to the negotiating table.

“Reacting publicly to the aftermath of what the agency knowingly spent in overtime on work they desperately needed instead of meeting with labor leaders to discuss concerns is shameful,” said Simon, general chairman of the Sheet Metal, Air, Rail and Transportation Union, which represents about half of LIRR laborers. “Unions play by the rules that are negotiated by both parties.”

Sen. James Gaughran (D-Huntington), who successfully pushed for the passage of a state law requiring the MTA to hire an outside company to perform a forensic audit on its finances, said he’s less concerned with overtime costs among LIRR laborers than he is with management costs inside the railroad’s “top-heavy administration.”

“In some cases, with rank-and-file employees, overtime is there because they just don’t have enough employees to cover shifts, or somebody gets sick and somebody runs in to cover,” said Gaughran, who believes the audit will result in new efficiencies and “management reforms.”