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A vulnerability to payroll abuse at the Metropolitan Transportation Authority is coming under the scrutiny of federal prosecutors in Manhattan after revelations that some employees were able to claim staggering amounts of overtime last year.

One worker at the Long Island Rail Road, asserting that he logged about 74 hours of overtime every week atop his regular duty, was paid $461,646 last year — more than the combined salaries of Gov. Andrew M. Cuomo and Mayor Bill de Blasio.

Federal prosecutors have subpoenaed pay records for that worker, Thomas Caputo, and more than a dozen other employees at the Long Island Rail Road and New York City Transit, according to three people with direct knowledge of the investigation. The three who spoke with The New York Times this week declined to be identified because they were not authorized to discuss it publicly.

Beyond those individuals, prosecutors plan to review the 19th-century time keeping practices used in some departments of the Long Island Rail Road: handwritten records submitted by employees.