The New York Metropolitan Transportation Authority’s interim executive director acknowledged Wednesday that extensive work to fix two major subway tunnels damaged by Hurricane Sandy would cost “hundreds of millions” of dollars.

But Thomas Prendergast expects full reimbursement for the work on the saltwater-damaged Montague and Greenpoint underwater tubes, which is expected to send commuters scrambling for alternative routes for at least 14 months.

“Our expectation is that we’ll be reimbursed by the [Federal Transit Administration],” Prendergast, standing alongside some damaged equipment, told reporters after Wednesday’s board of directors meeting in Manhattan.

The authority issued a statement later Wednesday saying it “expects expects no material
financial impact” from the tunnel work.

“The MTA’s current analysis projects that most subway customers affected by the tunnel closures will continue to use the subway system, transferring to alternate subway lines to complete their trips. The tunnel closure impact on overall ridership is expected to be negligible. No net losses are projected from fare revenue collection,” it said.

The cost of the work, including any incremental cost of providing service, will be charged to the
previously announced tunnel reconstruction projects, according to the MTA, which said that these projects were included in its capital plan amendment that the board adopted in February. That plan provides funding for Sandy restoration.

The Montague tube, a pair of 5,000-foot tunnels, carries the R train under the East River between Manhattan and Brooklyn. The shorter Greenpoint tube transports G train riders between Brooklyn and Queens under the Newtown Creek.

The MTA has estimated nearly $5 billion in costs related to the Oct. 29, 2012, storm, and expects federal and insurance reimbursements to cover most of it. Moody’s Investors Service rates the MTA’s transportation revenue bonds A2, while Standard & Poor’s and Fitch Ratings rate them an equivalent A. Authority officials declined comment on further cost specifics of the tunnel repairs.

“We’re not putting a price tag because we’re going out to bid,” said one spokesman, who said bid documents for the Montague tube work quoted more than $100 million. “Greenpoint, we can do a lot in-house.”

Montague will involve a general contractor and a separate signal contractor. Greenpoint will be in-house, with an outside signal contractor. The Montague tube, in far worse shape, will be closed for up to 14 months beginning early August. About 80% of it was flooded up to 20 feet with corrosive salt water sitting stagnant for 10 days. The MTA pumped more than 27 million gallons before even working to get the line running again in late December.

Acting N.Y.C. Transit president Carmen Bianco said customer delays due to Montague signal failures spiked after Sandy.

According to the MTA, working on the tube only on nights and weekends would delay its completion until 2017. “Fourteen months is a one-off,” said Prendergast. “This is the first time in my career that we’ve done something like this.”

The Greenpoint tube will be closed for 12 weekends this summer and fall starting July 6. There, power cables were corroding from the inside, while corrosion on the outside of the rails and fasteners heightens the risk of short circuits.

Prendergast likened the projects to building new tunnels from scratch. “It will take that long. Look at the mega-projects we have,” he said, citing the Second Avenue subway line, the No. 7 line extension and East Side access for Long Island Rail Road trains.

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