New York’s Metropolitan Transportation Authority, the largest U.S. transit agency, faces “credit strain” on its revenue bonds after state lawmakers lowered a payroll tax, Moody’s Investor’s Service said.

The state adopted the levy, along with higher fares, in 2009 to close a $1.8 billion deficit in the MTA’s budget. Governor Andrew Cuomo’s overhaul of the tax code, which the Legislature passed Dec. 8, cut the portion of payroll taxes paid by employers in the 12 downstate counties served by the MTA’s commuter trains.

The state has vowed to reimburse the MTA for the lost revenue without detailing how, Moody’s said Monday in a statement. The revenue will total $212 million next year and about $310 million annually thereafter, the ratings company said.

“The MTA’s financial operations are already tight, and failure to restore the lost revenue may put negative pressure on the MTA’s transportation-revenue bonds,” said Nicole Johnson, a Moody’s senior vice president and author of the report. “Our credit analysis will focus on how the state establishes a new backstop.”

The tax decision “signals a shift in government support” for the MTA and comes as the agency plans to increase borrowing to maintain and expand the transportation network, Moody’s said.

The bonds, known as TRBs, are rated A2, the sixth-highest level, with a stable outlook.

The MTA operates Metro-North, the Long Island Rail Road and New York City’s subway system.