Long Island Rail Road trains were late more often in 2015 than in any other year since 2000, LIRR statistics show.

The agency’s 2015 annual operating report, released last week, showed that on-time performance fell for the third straight year, to 91.6 percent in 2015 from 92 percent in 2014.

It was the worst year since 2000, when 91 percent of trains ran on-time.

The railroad, which carried a record 87.4 million riders in 2015, recorded declines in every on-time performance metric, including a 40 percent increase in the number of canceled trains, from 843 in 2014 to 1,260 last year.

In addition, trains that were forced to end their runs prematurely before reaching their destination rose by 29 percent.

The LIRR said many of the causes of service disruptions last year were out of their control, including problems in the Amtrak-owned East River tunnels, to track trespassers being near trains, major weather events and even a plane landing on the railroad’s tracks in August.

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In a statement, LIRR spokesman Salvatore Arena said that the railroad “is not satisfied with the recent trends, and is working to turn them around,” including through several infrastructure projects, like the Double Track effort between Ronkonkoma and Farmingdale and East Side Access, which will link the LIRR to Grand Central Terminal by 2022, and the recently resuscitated plan to build a third track on the Main Line between Floral Park and Hicksville.

“All these projects . . . will improve operational flexibility, service reliability, and on-time performance over the long term, but in the short term do create challenges for day-to-day LIRR operations and on-time performance,” Arena said. “But there is reason for optimism that over the long term, the work being done will influence trends in a positive way for many years into the future.”

Rush-hour trains were on time 88.9 percent of the time last year, down from 89.1 in 2014.

The biggest drop came on the Port Washington branch, where 91.8 percent of trains ran on time, compared to 93 percent in 2014.

Only the Montauk, West Hempstead and Babylon branches were more punctual in 2015 than in 2014, according to the figures.

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Rita Rosenfeld, who has been commuting on the Babylon line for more than two decades, found that increase “hard to believe.” Rosenfeld, of Massapequa, said cancelled trains on her line, and other major service disruptions have become a “routine” occurrence.

Recently, she paid $175 for an Uber ride home because an LIRR service problem caused Penn Station to shut down at the height of the evening rush.

“It’s insane,” Rosenfeld said. “It’s not OK to live like this. We’re paying $300 a month.”

The LIRR considers a train late if it arrives six minutes or more after its scheduled time. But the number of trains running 15 minutes late or more also grew by 17 percent. The average delay was 12.9 minutes, as compared to 12.2 minutes in 2014.

According to the LIRR stats, more late trains were caused by customers — 22.7 percent — than any other cause of delay. The category of “customers” includes delays caused by slow loading of trains in crowded conditions.

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Faulting customers for delays “ignores the fact that those riders are dealing with severe overcrowding and increased trains terminating at stops well before the final destination,” said LIRR Commuter Council chairman Mark Epstein, who called the LIRR’s 2015 punctuality figures “disturbing.”

Epstein said the LIRR’s worsening performance was evident in a recent event hosted by the Commuter Council that garnered unprecedented interest from riders.

“It was unbelievable, the amount of angst . . . I don’t think the railroad understands the depth of unhappiness,” Epstein said. “People are really tired of this.”

Addressing MTA Chairman Thomas Prendergast at a meeting of the State Legislature last week, Assemb. Todd Kaminsky (D-Long Beach) said he’s received “a rash of complaints” from constituents in recent weeks about LIRR service woes.

Prendergast acknowledged that “the past four or five months have been extremely troublesome” for the railroad, but noted that the LIRR has several capacity constraints that make it the most challenging of all MTA agencies to operate.

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“There’s an adage in this business: You’re only as good as your last rush hour . . . And we’ve had bad last rush hours,” Prendergast said. “People come to depend on that service. Where there are issues that are totally within our control . . . we’re making sure we we’re doing what we need to do to control those.”

Kaminsky said, despite the 182-year-old railroad’s limitations, the MTA should more proactively look for solutions, including by advancing a plan to centralize all of the LIRR’s train controls under one roof.

The LIRR, which controls trains from 11 different towers, says such a system is at least two decades away.

“People will live in the suburbs and pay the price of a ticket as long as they get to work and home in a reasonable fashion. But spending your time waiting in stations and waiting on the train is just an awful experience,” Kaminsky said. “The fact that it’s happening more is extremely troubling. We’ve got to turn this around.”

A pair of major winter storms in January and February, and a Hicksville freight train derailment in September alone were to blame for 1,463 late trains, or about 7 percent of the 20,689 recorded delays in 2015, according to the LIRR.