NEW YORK - The Port Authority of New York and New Jersey’s board of commissioners cited the need to maintain a high bond rating Friday morning in approving a set of toll and fare hikes for the region after the states’ governors softened the blow.

Citing a loss of $2.6 billion during the recession, capital plan expenditures that have outpaced revenues, and costs of overseeing the World Trade Center site exceeding $11 billion, chairman David Samson said: “These factors led Moody’s in January to change our outlook to negative.”

In a unanimous vote, the nine commissioners present among the 12-member panel — six appointed by Andrew Cuomo of New York and six by Chris Christie of New Jersey — ratified the increases, effective Sept. 18, that the governors signed off on Thursday night.

The adjusted $25.1 billion capital plan will help fund such projects as completion of the World Trade Center, raising the Bayonne Bridge roadway, rebuilding the Lincoln Tunnel helix and fixing the George Washington Bridge suspender ropes.

Tolls on cars using E-ZPass will go up $1.50 on Sept. 18 and then 75 cents each December from 2012 to 2015, down from the proposed $6 increase over four years at the request of the governors. Cars without E-ZPass must pay a $2 surcharge.

Fares on Port Authority Trans-Hudson, or PATH, trains will increase 25 cents annually over the next four years, as opposed to an immediate $1 increase.

The lower increases will reduce the Port Authority’s borrowing capacity by about $5 billion. The governors, in a joint statement issued Thursday night, also insisted on a “stringent audit” of Authority practices.

Earlier this week, New York Comptroller Thomas DiNapoli criticized the authority for failing to curb overtime costs. An audit by his office revealed that the agency paid $85.7 million for overtime during 2010 after making a commitment to reduce overtime costs by 20%.

Moody’s Investors Service affirmed the negative outlook for the Port Authority in March, when it sold $225 million of 167th series consolidated bonds.

Fitch Ratings and Standard & Poor’s both give the authority a AA-minus with a stable outlook.

The proposal, said Cuomo and Christie, “will prevent a default by the authority as well as a downgrading that would prevent the authority from borrowing money to pay for existing and future projects.”

The commissioners brushed past reporters after Friday’s vote.

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