Manhattan projects were awarded nearly $900 million in federal transportation money yesterday and the Senate voted overwhelmingly to double security subsidies for cities such as New York that are deemed likely terrorist targets.

But billions of dollars in federal subsidies for Metropolitan Transportation Authority projects remained in jeopardy because the MTA’s five-year capital plan has not received the necessary approval of the state’s Capital Program Review Board.

Mass-transit advocates warned Albany lawmakers in a letter yesterday that continued delay in approving the five-year capital plan, which includes detailing how a $2.9 billion transportation revenue bond on the ballot in November would be spent, could put at risk nearly $4 billion in federal funds earmarked for expansion projects, because the MTA must show that it can match those contributions.

The four-person review board failed June 30, for the second time, to reach the unanimity necessary to pass the plan.

The transit projects that received approval for large federal subsidies yesterday do not involve the MTA.

The Federal Transit Administration, an arm of the Department of Transportation, awarded $699 million to the Port Authority of New York and New Jersey for four projects related to rebuilding at the site of the World Trade Center. The bulk of the money, $478 million, is for the World Trade Center Security Center, an underground complex – south of the PATH station surrounded by Liberty, West, Cedar, and Greenwich streets – where some vehicles, such as tour buses and delivery trucks, will be screened for explosives.

Separately, the Department of Transportation awarded the state $200 million to rebuild a segment of the West Side Highway in Lower Manhattan between West Thames and Chambers streets.

The federal money is part of $4.55 billion appropriated by Congress for the redevelopment of Lower Manhattan, of which more than $3.86 billion has already been awarded.

In Washington, D.C., last night, senators voted 71 to 26 to approve an amendment introduced Monday, in response to the terrorist attacks in London, that would alter the formula to allot twice as much Homeland Security money to high-risk areas, such as New York. Previously money was allocated based only on population density.

Federal money for the MTA’s two most highly prized expansion projects, however, may be in doubt.

In February, the Federal Transit Administration gave its highest rating to those projects: the Second Avenue subway, and an extension of the Long Island Rail Road to Grand Central Terminal.

The ratings mean those projects would be given priority for federal mass-transit subsidies.

Without a capital plan detailing where the rest of the financing for the projects would come from, though, the subsidies could be lost to competing projects elsewhere in the country, a spokesman for the Regional Plan Association, one of 16 transit, labor, and environmental groups to sign the letter, said.

“States all over the country are licking their lips … ,” the spokesman, Jeremy Soffin, said. “Up to 50% … can be funded by the federal government on expansion projects, but that assumes you have your local share in place.”

Among the contracts put on hold by the MTA’s failure June 30 to win approval in Albany of its $21.1 billion capital plan was one, totaling almost $500 million, with a construction company, Slattery Skanska Inc., to bore part of a tunnel for the $6.3 billion project to connect the Long Island Rail Road to Grand Central Terminal, known as East Side Access.

Projects to improve New York City roadways are likewise suspended, since the capital plan of the MTA and the state’s Department of Transportation are approved simultaneously, the general manager of the General Contractors Association, Frank McArdle, said.

Also, a $138 million bid by the DeFoe Corporation to rebuild parts of the Brooklyn Queens Expressway near the Navy Yard in Brooklyn and a $25 million bid by another company, Acme Skillman, to repair parts of the Major Deegan Expressway near Yankee Stadium have been delayed because lawmakers have not agreed on unrelated issues in the capital plan, Mr. McArdle said.

“In this work, if you’re over 45 days, you can give the job back – you don’t have to hold the price,” Mr. McArdle said. “The 45 days was up June 6. They held the price but are unable to put people to work.”

Those projects will have to be re-bid, and most likely will cost more, he said.