SYOSSET - The MTA may have to raise train fares and bridge and tunnel tolls to make up for a $12 billion shortfall in its five-year capital budget.

State Comptroller Tom DiNapoli estimates the transit agency needs $27 million for new equipment and projects. DiNapoli also says the MTA may only be able to raise about half that amount in the next five years.

DiNapoli’s announcement is not sitting well with state Sen. Carl Marcellino (R-Oyster Bay) following assurances the Long Island Rail Road labor settlement would not be paid for by commuters.

“The clear promise was that there would be no need for a fare increase to cover any of the contract negotiations and any of the projects and programs that were on the books - they had the money," says Marcellino.

Despite commuters’ concerns, MTA Board Member Mitch Pally told News 12 Long Island that the comptroller's report does not necessarily mean fares and tolls will go up any more than the already projected 4 percent in 2015.

Commuter Michael Comerford was not comforted by assurances from the MTA.

"The MTA is like the bottomless pit of transportation," he said to News 12 Long Island.

The MTA Board will hold a meeting Monday afternoon to outline capital budget plans for the next five years and how to pay for them.