Amtrak's plan to build a new tunnel under the Hudson River into Penn Station will require the LIRR to move a critical train maintenance facility from Manhattan to Queens for more than two years, officials said.
Shifting maintenance operations from the Long Island Rail Road's West Side Yard to its Hillside, Queens, facility would put workers and resources farther away from any train breakdown in or near Penn Station for 26 months.
"If we had our druthers, would we be doing this? No," LIRR president Helena Williams said. "But we recognize that we're in a region where . . . intercity rail's future is extremely important, and we're cooperating."
Williams said the move is needed to accommodate Amtrak's Gateway Project, which includes new tunnels and tracks between Penn Station and Newark. One of those tunnels would run directly under the LIRR's maintenance facility on the yard's east side.
Although Gateway is not targeted for completion until between 2025 and 2030, construction on the tunnels needs to begin soon because Manhattan developer Related Companies plans to install structural supports in the same location for a commercial and residential project on top of the yard. The LIRR expects to make about $1 billion from a 99-year lease for the development.
Amtrak will reimburse the LIRR for moving expenses and increased operational costs at Hillside, and pay for demolishing the existing maintenance facility and building a new one at West Side Yard in the future.
"Building a new set of modern tunnels is essential to ensuring flooding like that seen during Hurricane Sandy won't again shut down the nation's busiest rail station," Amtrak officials said in a statement. Amtrak added the work will be done in cooperation with MTA and LIRR and it "hopes to begin construction on a concrete casing to protect this potential tunnel right-of-way in the summer of 2013."
Ira Greenberg, who represents the LIRR Commuter Council on the Metropolitan Transportation Authority board, said he believes the LIRR will do its best to minimize any impact on customers from the maintenance facility move, but is concerned about what could happen if repairs can't be made to trains near Penn Station.
"If you don't have enough equipment, we may have a short train or two during the rush hour," Greenberg said. "It's putting another strain on the operation of the railroad."
MTA board member Mitchell Pally, of Stony Brook, also expressed some frustration about how the construction work will inconvenience the LIRR.
"We have spent 20 years trying to get everything that the railroad could do into where they are now," Pally said. "The intent was to have them in Manhattan so that the operational needs of the railroad could be met easier."
An earlier version of this story misstated the completion date for Amtrak's Gateway Project, which is between 2025 and 2030.