Heaping overtime, payments stemming from union work rules and payouts of vacation and sick time for retiring workers added up to 22 percent of the money the Long Island Rail Road paid employees who worked a full year in 2009, an analysis of the LIRR payroll reveals.

The analysis of payments to 5,600 full-time employees shows the troubling financial picture at the nation's largest commuter railroad. The LIRR already has approved widespread service cuts and layoffs to help plug the Metropolitan Transportation Authority's unprecedented $800-million deficit.

Other findings include:

27 percent of the 5,600 employees who worked a full year in 2009 earned more than $100,000. That's more than any other MTA transit agency.

Among LIRR employees earning more than $100,000, the average union employee was paid $121,000. The average non-union employee, including managers, made $113,000.

139 LIRR employees doubled their salaries through extra payments, including overtime and so-called "penalties" for violations of union work rules.

Of union employees earning more than $100,000, 59 percent of their total compensation was for pay above their base salaries. For all LIRR employees, that figure is 27 percent.

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The analysis was based on figures compiled from LIRR payroll information released Wednesday by the Albany-based Empire Center for New York State Policy, an arm of the nonprofit Manhattan Institute for Policy Research. The figures include employees who were given one-time payments of sick days and vacation time as they retired.

In a statement Thursday, LIRR officials said the agency "is working hard to reduce costs by making headcount and overtime reductions."

"We are in a fiscal crisis and we need to make every dollar count," the statement said.

MTA officials have said they must bring down overtime and costs resulting from "outdated" and "cumbersome" union work rules.

MTA board member Mitchell Pally, of Stony Brook, said all LIRR union contracts expire June 30, and language regarding work rules and overtime payments will have to be addressed by the agency.

Anthony Simon, chairman of the United Transportation Union, which represents the LIRR's conductors, said that his colleagues work overtime when they are called to do so, and that the LIRR's recent and impending layoffs only serve to increase the overtime costs.

Nearly half of the employees who doubled their salary with payments beyond base pay were from three job categories: 33 conductors, 16 engineers and 14 train-car repairmen.

A conductor's base salary in 2009 was $75,389. But the average total earned by a conductor last year was $122,175 - 38 percent over base pay.

Simon declined to discuss union work rules.

MTA Board Chairman Jay Walder and the board "have made clear" that issues such as workers earning double their salary in overtime and other payments need to be reviewed, Pally said. Contracts that govern payments beyond base pay were negotiated during less severe economic times, he noted.

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Gerry Bringmann, vice chairman of the Long Island Railroad Commuter Council, said contracts negotiated by former MTA managers are coming back to bite the agency. He called workers doubling their base salary with overtime "a shame" because it illustrates "a failure" of management.

"You've got people making these kind of salaries but they're closing my ticket office next month," Bringmann said.