The feds are investigating Long Island Rail Road workers amid an overtime explosion — including one who made $344,000 in extra pay by clocking a seemingly impossible number of hours, it was revealed Friday.

The Manhattan US Attorney’s office has subpoenaed pay records for more than a dozen LIRR employees, according to The New York Times.

Among them is reigning overtime king Thomas Caputo, whose 3,864 OT hours in 2018 were outlined in a series of Post reports about skyrocketing payroll costs at the railroad, sources told the Times.

The federal investigation also will examine the LIRR’s archaic practice of using handwritten time sheets — even though more modern systems are available.

“We do have systems where it is on paper,” LIRR president Phil Eng explained at an emergency MTA board meeting on the OT payments last week.

“The employee fills out the forms, the supervisors review, and administratively they get it into the system.”

The MTA is attempting to introduce a unified, agency-wide timekeeping system that would incorporate biometric checks such as fingerprinting.

Workers, however, are unhappy with the more modern machines, the Times reported.

MTA chairman Pat Foye promised the “rapid rollout” of a 21st century system after the Empire Center for Public Policy revealed the staggering overtime hours logged by Caputo and others.

Caputo, the recently retired chief measurement operator, brought home a $461,646 paycheck in 2018 — more than anyone else at the MTA, according to data released by the Empire Center.

Caputo clocked in almost every weekend and averaged 15 hours a day, the MTA said.

On top of his sizable salary, Caputo will likely score a $162,000 annual pension, which ballooned by $93,000 as a result of his total pay over the last three years.

Another LIRR employee, track worker Marco Pazmino, raked in $256,177 in overtime pay for 2018, despite earning a base of just $54,985 — bringing his haul for the year to $311,162.

The MTA spent $1.3 billion in overtime in 2018, up more than $100 million from the previous year.

The Queens District Attorney’s Office and the MTA’s inspector general also are probing overtime at the LIRR.

The investigation is reminiscent of the LIRR’s $1 billion “Gravy Train” pension fraud scandal that sent three men to jail for eight years in 2012.

The scam came to light when it emerged that nearly every LIRR member who requested a disability pension was awarded one.

Employees were allowed to choose their own doctors, who then approved the fake disability for the additional pension.

A number of LIRR employees received probation in the scheme after cutting deals with prosecutors.

© 2019 the New York Post