New York State Comptroller Thomas DiNapoli, March 14, 2012.

New York State Comptroller Thomas DiNapoli, March 14, 2012. Credit: Newsday / Audrey C. Tiernan

ALBANY -- The MTA let millions of dollars sit idle in bank accounts rather than boost investments or pay costs, according to an audit released Wednesday.

State Comptroller Thomas P. DiNapoli chided the Metropolitan Transportation Authority for not consolidating $90 million held in separate funds, saying it did a "poor job of managing its cash-on-hand." The audit came just weeks before the transit agency will implement its fourth toll and fare hike in five years.

"The MTA is leaving money on the table and in these tough times, every dollar counts," DiNapoli said in a statement with the audit. He added that the agency didn't have a written investment plan -- making it impossible to know if it met expectations.

The audit covered MTA's cash management from Jan. 1, 2008, to March 31, 2011. Of 101 accounts the comptroller's office examined, 45 had balances of more than $1,000. By MTA policy, monies from certain accounts with four-digit balances or greater should be forwarded to the agency's treasury for investing.

An MTA spokesman said the agency was in the process of consolidating accounts when the comptroller's audit got under way. Spokesman Adam Lisberg added that some accounts are maintained to protect credit ratings.

"The office of the state comptroller has questioned whether the MTA has excess funds in several accounts, particularly a Triborough Bridge and Tunnel Authority reserve fund," Lisberg said in an email. "Monies in this account are essential to maintaining our credit rating, and are available in the event of emergencies such as superstorm Sandy."

Higher transit fares will kick in March 1. Long Island Rail Road fares will rise between 7.1 percent and 15.3 percent, depending on the ticket type and distance traveled. The increase on each ride would be limited to 75 cents.

The base fare on city subway and buses will climb to $2.50 from $2.25, although customers purchasing a single-ride MetroCard will be charged $2.75.

The MTA has said it intends to raise $450 million in new revenue each year. Most of increase would go toward rising employee pension and benefit expenses, officials have said.

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