Gov. Andrew Cuomo’s ambitious plan to replace the aging Tappan Zee Bridge has quietly hit financial uncertainties that could shift more of the $3.9 billion cost to motorists and taxpayers statewide, with the possibility of far higher tolls than the $14 originally predicted, according to documents and interviews.

That’s because the state stands to receive a federal loan for much less than Cuomo originally sought. He asked a year ago for a loan that would cover 49 percent of the project, but the federal government told the state this past week that the biggest loan it would get would be 33 percent.

At the same time, the state Thruway Authority’s credit outlook, which can affect borrowing costs, recently received a “negative,” in part because of its $3.7 billion debt and its refusal to reveal a plan for toll hikes.

All of that mean the state will have to finance more of the project with traditional loans at higher rates than the low-interest money offered by the government. And other sources — such as bridge tolls, statewide Thruway tolls and state money — could be tapped to cover those higher borrowing costs.

“I suspect that most of the increase will be on the bridge itself, but I wouldn’t be surprised if there was a bit of an increase elsewhere to help pay for it,” said Peter Samuel of the national trade magazine Toll Roads News, which has followed the project closely. “It’s quite possible they will try to spread the pain about.”

What that means for the 170,000 motorists who cross the Hudson River interstate span north of New York City every day is unclear.

The toll for the current Tappan Zee is $5. And the Thruway Authority estimated last year — under the previous hopes for federal funding — that when the new bridge is completed in 2018, the toll could nearly triple to about $14, which Cuomo said was too high.

Thruway spokesman Dan Weiller refused to provide an estimate for toll increases or to say if the project’s costs would be extended statewide to Thruway highway tolls.

But he added that once the terms of federal funding are finalized, “a Toll-Financing Task Force will begin a process to keep tolls as low as possible.”

Thruway Authority Executive Director Thomas Madison said last week that he was optimistic about getting the federal loan but said for the first time that the authority is prepared to borrow the money elsewhere if the loan isn’t approved at all or for the full amount requested. The state is asking for $1.5 billion.

The U.S. Department of Transportation this week said it is still evaluating the state’s funding plan, which will use tolls to repay any loan.

Charles Komanoff, a Manhattan economist and transportation researcher, has predicted tolls would have to rise significantly and could spread to Thruway users statewide. He declined to hazard a guess on just how they could go.

E.J. McMahon of the Empire Center for Public Policy said all taxpayers may be forced to help pay for the bridge replacement. He noted Cuomo set a precedent a year ago to avoid a politically unpopular 45 percent increase in commercial vehicle tolls by tapping the state’s general fund.

“He set a precedent and it’s a very bad one,” McMahon said. “The Thruway Authority is not healthy, and it doesn’t look good even without the Tappan Zee replace on their books … where’s the financial plan?”

The lack of toll plan has resulted in a “negative” outlook for the project by the state’s rating agency, Standard & Poor’s. The August rating report says the negative outlook is because toll increases discussed so far and spending cuts might not be enough to support the Thruway Authority’s existing $3.7 billion debt and taking on the Tappan Zee replacement.

Adding to the cost is $700 million the authority borrowed in September to provide cash flow on preparation work and to pay back $500 million borrowed in February.

“At this point, we’re closely monitoring the situation,” said Joseph Pezzimenti, primary credit analyst with Standard & Poor’s. “The negative outlook is because we haven’t received plans on what their tolling plan should be.”

© 2013 Associated Press