The Metropolitan Transportation Authority, which hiked fares for riders this month, paid one employee more than $344,000 in overtime in 2018 in addition to his $117,499 salary, according to data released this week by a fiscal watchdog group.

The transit agency last year paid its workers a total of $418 million in overtime, a 16 percent increase from a year earlier, according to the Albany-based Empire Center for Public Policy.

A database of employee salaries, with overtime, shows the top 10 earners pulled in more than $350,000 each, and seven of them worked for the Long Island Rail Road, which is operated by the MTA.

The MTA disputed the extent to which overtime pay and total payroll increased in the data. Empire said its figures came after reviewing worker payments labeled overtime from a Freedom of Information Law request.

The top earner in the report was Thomas Caputo, a chief measurement operator for the LIRR who pulled in more than $344,000 in overtime on top of his $117,499 annual salary, bringing his total compensation to $461,646, according to the database.

“The collective bargaining agreement and its rules about seniority allow those with the most years on the job to get first pick at overtime opportunities,” said Max Young, an MTA spokesman. “We are absolutely committed to reducing spending, including a hard target of an additional $500 million in annual savings across all MTA agencies next year.”

The overtime spending came during a year in which the LIRR saw its worse on-time performance percentages in nearly two decades.

Caputo, who retired this month, could not be reached Thursday for comment. Caputo drove the advanced track geometry car, operated the inspection equipment and maintained the car, the MTA said.

The LIRR’s overtime spending increased $50 million — almost 30 percent — from $175.4 million in 2017 to $224.6 million in 2018, according to the Empire Center, a nonprofit that annually breaks down payroll of the MTA.

Fifty-eight of the 100 highest-paid MTA employees in 2018, including the top four, worked for the LIRR, according to the report. Pay included overtime and other extra pay, such as shift differentials.

The two other highest-paid hourly employees for the LIRR were surfacing foreman Dallas Bazemore III, at $395,397, and track foreman Joseph Ruzzo, at $380,407. In salaried management positions, the three highest paid were Patrick Nowakowski, former agency president, at $454,288; Phillip Eng, current LIRR president, at $294,243; and Afshin Hezarkhani, chief engineer of special projects, at $260,380.

“Sixty percent of MTA costs overall are on personnel. And when those costs go up, you either have to collect more money or do less. It makes sense to focus the conversation on that,” said Ken Girardin, a policy analyst at the Empire Center. “Overtime is a normal part of managing any organization. There will always be overtime. But when you see a jump in overtime, it’s worth noting.”

LIRR employees on average earned $34,000 in overtime pay last year, 50 percent more than 2017’s average of $22,701, according to Empire’s report. LIRR payroll spending last year grew by more than 10 percent, or $84 million.

Since 2008, the railroad has increased payroll spending by $280 million, or 45 percent. At the same time, the number of employees increased by 9.6 percent. LIRR employees were paid an average of $112,404 last year, compared to $84,484 in 2008.

Overall, the MTA spent more than $7 billion on salaries and wages for its 80,057 employees in 2018. Shams Tarek, an MTA spokesman, said in an email that payroll rose $238 million, from $5.7 billion in 2017 to $5.938 billion last year. Overtime costs, meanwhile, increased by $122 million, from $1.202 billion in 2017 to $1.324 billion, he said.

The MTA’s payroll increase comes as the agency tries to cut costs amid a dire budget forecast. It expects a billion-dollar budget gap by 2022 — even with another fare hike planned for 2021. The costs also come as the MTA aggressively targets fare evaders, calling for more police to catch people who don’t pay on city buses and subways. Fare evasion cost the MTA $225 million last year, according to the authority.

Tarek reasoned that overtime is often more cost-effective than hiring full-time workers.

“In the meantime, the MTA is undertaking very aggressive cost-cutting measures across all agencies, achieving more than [$2 billion] in recurring savings with a target for an additional $500 million of savings next year,” Tarek said in a statement. “We’re also undergoing reforms, including a forensic audit, consolidation and reorganization, a reduction in construction costs across the system, and ultimately the net savings will be far greater than any investments being made to achieve these major improvements.”

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