Amtrak officials said on Wednesday that they will have to sharply curtail use of the century-old rail tunnels leading to New York City for at least a year to repair the damage caused by Hurricane Sandy, a move that would affect train service for tens of thousands of commuters.

One of the four tubes that carry trains under the East River between Manhattan and Long Island would be the first to close, possibly in late 2015. The work on that tube would take a full year and would affect service on the two railroads that also use the tunnel, the Long Island Rail Road and New Jersey Transit, which uses a rail yard in Queens to park its trains.

Floodwaters from the storm two years ago inundated two of the four tubes of the East River Tunnel and both tubes of Amtrak’s two-track tunnel under the Hudson River. Eventually, Amtrak will need to shut each of the four damaged tubes to fix the extensive damage caused by the saltwater, said Stephen Gardner, Amtrak’s vice president for Northeast Corridor Infrastructure and Investment Development.

Closing and overhauling the tubes, one by one, was among the recommendations in a report that Amtrak commissioned and planned to make public on Thursday. The report, which details all of the damage caused by the storm, estimated the total cost of repairs at $689 million.