The Long Island Rail Road came under fire Monday from riders and their advocates after failing to restore service by 5 a.m. as promised on seven of its 12 lines, and issuing confusing updates to tens of thousands of commuters.

LIRR officials had pledged to get 80 percent of the system up and running in time for the morning rush, but that did not happen. Instead, riders faced major delays and confounding communications from railroad officials while waiting for trains.

Rail safety experts said LIRR officials underestimated the severity of Saturday’s storm, which dumped more than 2 feet of snow on the nation’s largest commuter railroad.

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In its effort to recover Monday, the LIRR suffered numerous setbacks. Besides delays, lines that did run saw overcrowding and numerous cancellations, as the railroad continued dealing with snow-packed third rails and track switches that froze overnight from Sunday into Monday morning.

As of Monday evening, the LIRR was still operating on just seven of its 12 lines, with no trains running on the Long Beach, Far Rockaway, Hempstead or West Hempstead branches, or to and from Brooklyn.

“This historic superstorm hit areas of Long Island with nearly 30 inches of snow, and that kind of volume presents unique challenges to any clean up effort,” LIRR spokesman Aaron Donovan said.

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About 5 a.m. Monday — the time the LIRR said it would resume normal service on its four busiest lines — the agency announced it would not be ready to run trains until 7 a.m., and not at all on one of those branches, Port Washington. Service on that line finally came back about 3 p.m.

At a regularly scheduled Manhattan meeting of the Metropolitan Transportation Authority’s LIRR Committee, railroad officials had little to say about the disruptions, other than to promise a report on the agency’s handling of the storm at its next meeting in February.

LIRR President Patrick Nowakowski originally planned to address the situation at the meeting, but did not show because he was “out restoring service this morning, making sure it’s all done,” according to committee chairman Mitchell Pally.

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The LIRR had shut down service about 4 p.m. Saturday, but not before 10 trains became disabled in the rapidly mounting snow. On Sunday, Nowakowski acknowledged that the LIRR may have erred in not shutting down sooner, and said the stranded trains hindered the LIRR’s ability to restore service.

MTA Board member Ira Greenberg said stranding riders on trains for hours is unacceptable.

“We’re going to have to take a good look at that,” Greenberg said. “They can’t do that.”

Moriches railroad safety consultant Carl Berkowitz said “human error” was likely behind the LIRR underestimating Saturday’s storm. “The Long Island Rail Road should know what their equipment can handle or can’t handle.”

Meanwhile, the LIRR’s chief watchdog group said it was “extremely disappointed” in the railroad’s communication efforts throughout the first post-storm commuter day. LIRR Commuter Council Chairman Mark Epstein noted that agency alerts and announcements did not reflect actual service levels.

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“When weather conditions disrupt service, the LIRR’s communication with riders must be timely, accurate, and clear,” Epstein said.

Donovan said the LIRR did its best to provide real-time information to riders under rapidly changing circumstances.

Gov. Andrew M. Cuomo, who coordinated Saturday’s travel ban in New York City and Long Island, which included the LIRR shutdown, on Monday defended the railroad’s efforts to try to bounce back.

“I knew they were working very, very hard because I talked to MTA, LIRR employees who’d been working literally for days,” Cuomo said. “My guess is they ran into more complications than they expected when they actually put the trains back in service.”

Officials with Cuomo’s office said he acted “swiftly” based on the recommendations from the LIRR. They said were it not for Saturday’s shutdown, there may have been no LIRR service at all Monday.

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But LIRR commuter Jacob Lafond, 30, of Mineola, said there was no excuse for the LIRR’s service woes. “It’s very disheartening that my streets are plowed, but my trains aren’t running.’’

Sen. Chuck Schumer (D-N.Y.) also weighed in on the LIRR’s lingering issues Monday, saying he would have liked to see the railroad clean up the system “as quickly as possible. And, obviously, that hasn’t happened.”

“I’d like to get an explanation as to why it takes as long as it does,” Schumer said at an unrelated news conference. “We don’t have all the lines working today. Every day that people can’t get to work, the New York metropolitan area and Long Island suffers.”

With Yancey Roy and Chau Lam