The Long Island Rail Road is making progress on repairing, rebuilding and hardening its system devastated four years ago by superstorm Sandy, officials said.

However, they say some projects are still years from completion, including several along the LIRR’s vulnerable Long Beach branch.

The railroad’s post-Sandy improvement efforts have been focused on the four areas hit hardest by the October 2012 storm — rail yards in Long Island City and on Manhattan’s West Side, the East River Tunnels leading into and out of Penn Station, and the Long Beach branch, which residents and officials say may never fully be out of harm’s way.

“When Superstorm Sandy roared across the New York/Long Island region . . . the effects were devastating, but preparation paid off,” said LIRR spokesman Salvatore Arena, adding that the railroad’s pre-emptive shutdown before the worst of the storm allowed it to move trains to higher ground to protect them. “However, although LIRR personnel planned carefully for Superstorm Sandy, there was substantial damage to the infrastructure due to greater-than-expected storm surge.”

Some efforts have already made considerable progress.

New electrical substations — elevated to protect them from flooding — have already been installed in Long Island City, near the East Rockaway station and in the Oil City section of Oceanside. A contractor has finished 13 of 15 new elevated platforms, which will protect new signal and communication huts from flooding.

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Improvements to the Wreck Lead Bridge, which carries the LIRR over Reynolds Channel, are well underway and expected to be finished by April. The bridge has already gotten a new emergency generator, walkway lighting, high-tension poles and other electrical equipment.

Other improvements, however, are far from being finished.

The Metropolitan Transportation Authority Board on Friday awarded a $2.4 million contract for new signal equipment for the Long Beach line — part of a broader effort to replace signal, switch, communications and third rail equipment along the line that isn’t expected to be completed before September 2019.

“There’s still a lot of work that needs to be done. But then again, a lot of work has been done,” said John Molloy, the Nassau County representative on the MTA Board. “I think the MTA has done nice work moving this thing along . . . You just can’t do it overnight. It’s a lot of work, and a lot of pieces that have to be put together. ”

Nowhere did the LIRR’s system get hit harder by Sandy than on the Long Beach line, where tracks and delicate electrical components were submerged under 4 feet of corrosive saltwater and sewage, three electrical substations were damaged, and nearly two dozen boats and personal watercraft washed up on tracks.

It took nearly a month for the LIRR to restore full service on the line, used by more than 20,000 riders each weekday.

“It was very difficult. We were the last [LIRR line to be restored.] It’s highly insulting, but what can you do about that?” said Island Park Mayor Michael McGinty, who commended the LIRR for its work modernizing electrical substations on the line, but said the agency hasn’t done enough to seek input from local government on the problems facing local commuters, including over drainage. “The line is very important to the residents of Island Park, as well as Long Beach, Lido Beach, Point Lookout and, believe it or not, some from Oceanside.”

Fran Kravitz, who commutes from Island Park for acting classes and jobs in Manhattan, recalls her husband having to move into Manhattan for weeks after Sandy because of the service problems on the Long Beach line.

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Four years later, Kravitz, 56, said the branch remains particularly susceptible to flooding.

“If we get a storm on a full moon in high tide, those train tracks are under water . . . The tracks are still on the ground, so it’s still going to flood, just like the rest of Island Park.”

William Henderson, executive director of the MTA’s Permanent Citizens Advisory Committee, which includes the LIRR Commuter Council, said although the MTA has done substantial work to repair and fortify its system over the last four years, the work may never be fully done, in part because it will have to keep up with rising sea levels and other major weather events.

“I think they’re going to be doing hardening for years — probably for our lifetime,” said Henderson, who singled out the Long Beach line as a particular challenge. “At the end of the day, you’ve got tracks that are going over and basically next to water. If there’s a storm that comes up and across the water, there’s going to be impacts.”

Other flood-prone parts of the LIRR’s territory are also in line for improvements. The LIRR is putting $100 million in Federal Transportation Administration grant funding toward several planned projects to fortify its West Side Yard, the Queens portals of the East River Tunnels, and the tunnels themselves. Those efforts are in their early stages, with the MTA currently working out cost estimates, officials said.

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The LIRR has also begun flood-protection work on its Atlantic Avenue tunnels along its Brooklyn line and at the Long Island City yard.

The Federal Transportation Administration also in June awarded the MTA $432 million to make critical repairs inside the East River Tunnels, which were badly damaged by corrosive saltwater from Sandy flooding. Amtrak, which owns the tunnels and is responsible for the repairs, has said the work won’t begin until the end of this decade, and take several years to complete.