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One night two years ago, Thomas Caputo, a senior track worker for the Long Island Rail Road, put in for 15 hours of overtime for work he said he had done at the West Side Yard in Manhattan. His shift began at 4 p.m. and ended at 7 o’clock the next morning.

But, the authorities say, Mr. Caputo was somewhere else that evening: at a bowling alley in Patchogue, N.Y., more than 55 miles away, where he bowled three games, averaging a score of 196.

He took home an overtime payment of $1,217, the government said.

Mr. Caputo was one of five current and former employees of the Metropolitan Transportation Authority charged on Thursday with participating in an overtime fraud scheme that allowed them to become among the highest-paid employees at the agency, federal prosecutors in Manhattan said.

The defendants, who worked at the Long Island Rail Road and New York City Transit, frequently volunteered for lucrative overtime shifts and later claimed they had worked when they were in fact at home or other nonwork locations, or even on vacation, the prosecutors said.

Audrey Strauss, the acting U.S. attorney in Manhattan, characterized the scheme as brazen and involving claims for “extraordinary, almost physically impossible, amounts of overtime.”

Mr. Caputo, 56, who retired in 2019 after three decades with the railroad, was listed in 2018 as the highest paid M.T.A. employee with total pay of more than $461,000, including about $344,000 in overtime. All five defendants each earned more than the salary of the M.T.A. chairman or Gov. Andrew M. Cuomo, who oversees the agency.

A lawyer for Mr. Caputo did not immediately return a message from a reporter seeking comment.

In 2018, according to a criminal complaint unsealed on Thursday, Mr. Caputo claimed to have worked 3,864 overtime hours, on top of 1,682 regular hours.

If he had worked every single day that year (which he did not), the complaint said, his claims would average about 10 hours of overtime each day for the entire year, beyond his regular 40-hour workweek.

He and the four other defendants each earned more than $348,000 total in 2018, the authorities said. The others ranked fourth, fifth, 11th and 12th that year in pay among all M.T.A. employees.

The charges come at a time when the authority is confronting its worst financial crisis because of the pandemic and a stalemate over federal aid. Without a financial bailout, the agency has said that it will have to slash subway and bus service and that more than 9,000 workers could lose their jobs.

The five defendants were expected to appear before a federal magistrate judge in Manhattan on Thursday afternoon.

The New York Times reported in May 2019 that the prosecutors had subpoenaed pay records for Mr. Caputo and more than a dozen other employees at the Long Island Rail Road and New York City Transit.

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