Overtime pay at the agency running New York City's transit is going off the rails. As the Metropolitan Transportation Authority (MTA) is railroaded by stalled schedules, busted budgets and a fare hike for riders, the agency paid its workers $418 million in overtime last year — including more than $344,000 for a single employee.

A study released Tuesday by the fiscal watchdog Empire Center said the MTA's overtime rose nearly 16 percent in 2018. The $418 million in overtime it paid last year is $82 million more than MTA expects to raise each year from its latest round of price hikes for customers.

The MTA operates New York's subways and buses, in addition to the Long Island Rail Road (LIRR), Metro-North Railroad and Staten Island Railway.

Inside the New York City subway

Get Breaking News Delivered to Your Inbox Click here to view related media. click to expand

A database of employee pay shows that, with overtime, 20 workers earned more last year than Andy Byford, who oversees the entire New York City Transit Authority. Thomas Caputo, chief measurement operator for the LIRR, received $344,146.93 in overtime on top of his $117,499 salary, bringing his total compensation to $461,646.

It's not clear how many overtime hours Caputo clocked or what his overtime pay rate is. The database lists his regular rate of pay as $54 an hour.

The database shows that most of the MTA's top earners cleared more than $320,000 in 2018 and work for the LIRR. This came during the year that saw the LIRR's worst on-time performance rates in 19 years.

By comparison, Byford earned $313,468 last year — which is less than his listed pay rate of $325,600.

MTA chairman Patrick Foye said some of the overtime came from repairs that are done on nights and weekends to help the system's crumbling infrastructure. But he said the MTA had hired an outside consultant to help find $500 million in savings by the end of 2020. "We're committed to reducing expenses at the MTA across the board," Foye told CBS New York. "We can and must do better." The database says Foye received $347,707, meaning the chairman wasn't even in the top 10 earners.

The watchdog report comes after the MTA rolled out another round of fare hikes. On Sunday, the agency raised the price of weekly MetroCards in New York City from $30 to $33, while monthly passes increased from $121 to $127. LIRR weekly tickets jumped to $5.75 and monthly tickets to $15. Tolls on many bridges and tunnels also increased about by 36 cents.