Comptroller Thomas DiNapoli said Monday he'll conduct a forensic audit of Metropolitan Transportation Authority overtime spending to search for criminal wrongdoing among the agency's employees.

The audit will piggyback off one DiNapoli issued earlier this month that found MTA overtime costs increased 26 percent between 2005 and 2009, when the MTA paid $560 million in overtime. His investigators will look specifically for evidence of criminal fraud and wrongdoing, his office said.

"Some of what we saw raised the question of whether this is a need to tighten our practices or whether there was wrongdoing going on," DiNapoli told Newsday. "Was this overtime in fact happening or did you have a case of wrongdoing or fraud?"

DiNapoli said that if the forensic audit finds specific MTA employees defrauded the system to get paid overtime they did not work, he will refer the cases to the local district attorney or the attorney general's office. Three-quarters of overtime transactions in the initial audit lacked justification or came with undocumented work, DiNapoli said.

"Overtime expense has been growing at the MTA," he said. "We think this is an area that the MTA will benefit from our continued oversight."

The audit comes as the MTA struggles with a $900-million budget deficit and riders face service cuts and a 7.5 percent fare hike looming in January.

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DiNapoli's MTA audit of Aug. 5 found that the Long Island Rail Road dedicated a larger segment of its budget - 17 percent - to overtime than did New York City Transit, Metro-North and the MTA Bridges & Tunnels agency.

That study concluded that in 2009 the four highest earners of overtime among the MTA's 7,100 workers - and 11 of the top 16 - came from the LIRR.

And a September audit found lax oversight of MTA overtime, which included some low-level supervisors signing off on their own overtime.

In May, MTA chairman Jay Walder announced plans to cut overtime by $60 million next year through a combination of better management controls and collective bargaining with unions, whose contracts and work rules regulate how overtime is paid.

MTA spokesman Jeremy Soffin said the agency will cooperate with the audit. "We welcome the comptroller's assistance as we continue to fulfill our commitment to reduce overtime," he said.

DiNapoli, appointed comptroller in 2007, faces Republican Harry Wilson of Scarsdale in his first run for statewide office in November.DiNapoli declined to say whether the forensic audit would be complete before Election Day.