Salaries at the agency that operates the city's subways and buses have increased for the second year in a row, even as service cuts and layoffs loom.
Data released Wednesday by the Empire Center for New York State Policy, a nonpartisan research organization, show salaries and total payroll increased by more than two percent in 2009.
More than 10 percent of employees made at least $100,000 a year, while the average pay for an employee was just under $70,000. Total payroll was just under $5.2 billion in 2009, up from $5.1 billion the year before.
The Empire Center is a project of the Manhattan Institute for Policy Research, an Albany think tank.
Lise Bang-Jensen, a senior policy analyst for the Empire Center, said that high salaries are a result of union contracts that allow sick time and vacation to be carried over from one year to the next and in some cases "excessive" overtime.
The Metropolitan Transportation Authority "agreed to these rules in the past," Bang-Jensen said. "Whether they can afford to continue these practices in the future is the question."
Among the top 10 paid employees was a Long Island Rail Road conductor who earned almost $240,000, though his base pay was only $75,390. The average salary for all 886 conductors on Long Island was just over $100,000.
LIRR spokesman Joe Calderone said the conductor's higher salary was because he retired in October after 35 years.
"It was a combination of straight time, overtime and unused vacation and sick time he had saved up," Calderone said. "This was a one-time payout."
MTA spokesman Kevin Ortiz said the overall increase was due to raises already promised to unions.
"All of our managers had their wages frozen last year," he said.
The MTA has said it has an $800 million budget shortage, which will result in the elimination of 3,000 jobs this year out of its nearly 75,000 employees.
Service cuts and layoffs are expected at the end of June.