The Queens entrance to the East River Tunnels that flooded...

The Queens entrance to the East River Tunnels that flooded during Superstorm Sandy in October 2012. Credit: Amtrak

A long-awaited effort to repair Superstorm Sandy tunnel damage will result in fewer LIRR trains serving Penn Station, the railroad’s president said Monday.

But the restrooms on those trains may be more sanitary than usual, thanks to a new cleaning protocol, Long Island Rail Road president Robert Free also announced.

Amtrak’s forthcoming repair of the two East River tunnels that were damaged by floodwaters in the October 2012 storm will require the LIRR to operate with one fewer tube going into and out of Penn Station for 30 months.

The tunnel work will begin on Nov. 11, the same day the railroad’s new timetables take effect.

Speaking at a Manhattan meeting of the Metropolitan Transportation Authority board’s railroad committee Monday, Free said, because of an “intense but collaborative dialogue” with Amtrak, and because of the redundancy that the railroad added with the opening of a second Manhattan terminal, Grand Central Madison, last year, the project’s impact on LIRR service will be “minimal.”

Two morning rush hour trains that usually go to Penn will instead be diverted to Grand Central Madison, according to the LIRR. Several other trains will have their times adjusted by up to 27 minutes.

“We will continue to monitor and make adjustments as necessary as this momentous project progresses,” said Free, who noted the railroad “demanded to Amtrak as minimal impact to our customers as possible.”

Amtrak spokesman Jason Abrams said in a statement Monday that Amtrak, the LIRR and NJ Transit, which also operates out of Penn Station, “are coordinating closely to mitigate service impacts and will provide detailed service information via numerous channels in the coming months.”

The $1.6 billion tunnel repair project, which is being primarily funded by the federal government, will entail demolishing the tubes to their concrete liners, then rebuilding them with several structural improvements, including "bench walls" that train passengers can walk on during emergency evacuations. New signal, drainage and fire and smoke detection systems will also be installed, Amtrak has said.

LIRR officials said there will be no changes in overall service levels or travel times to and from Manhattan, and no changes to weekend schedules. The new timetables include other changes unrelated to the tunnel work. Full schedule information is available on the MTA’s TrainTime app and at the LIRR’s website, www.mta.info/lirr.

The LIRR on Monday also announced a new initiative aimed at improving the cleanliness of train restrooms. A program begun earlier this year allowing customers to scan QR codes in station restrooms to report any issues will be expanded to train bathrooms, Free said.

Posters with the QR codes linking to a “restroom survey” will be put up on all LIRR train car restrooms by the end of this year, according to the railroad.

Since the posters started going up on station restrooms in July, LIRR customers have submitted more than 230 surveys “alerting us to stations that needed some cleaning or that had run out of supplies,” Free said.

Get the latest news and more great videos at NewsdayTV Credit: Newsday

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