The Long Island Rail Road is hoping to return to normal service in time for the evening commute after a major service disruption at the peak of the morning rush hour Wednesday.

The LIRR is still reporting lengthy residual delays averaging 90 minutes on several trains after an Amtrak-related signal problem just east of the East River rail tunnels caused the LIRR to suspend service into and out of Penn Station.

LIRR spokesman Aaron Donovan said the railroad learned of the signal problem, which it attributed to a "power outage," about 5 a.m. By 7:45 a.m., the LIRR had shut down all service into and out of Penn, canceling several trains and diverting others to the Atlantic Terminal in Brooklyn. New York City Transit cross-honored LIRR fares on several subway lines.

The service problems resulted in large crowds at Jamaica station, and also stalled tennis fans heading to the U.S. Open on the LIRR's Port Washington line, popular among tennis fans bound for the event in Flushing Meadows.

Gov. Andrew M. Cuomo, at an unrelated Greenwich Village event, said upgrades to the transit system, including the LIRR, must be made.

"It is urgency is there, obviously. It's a very big system, and issues come up," he told reporters, saying investing in the Metropolitan Transportation Authority's "robust" capital plan is important to avoid "continued issues."

"It's time, and I'm willing to invest the money from the state side and I've asked our partners in local government to also help," he added.

Shortly after 9 a.m., the LIRR announced that it would restore "limited service" into and out of Penn Station and on the Port Washington branch. Still, the delays caused by the "cascading effect" of backups persisted. Shortly before 11 a.m., the LIRR was still reporting delays of as much as 2 hours and 24 minutes.

"This took place at the height of the rush hour," Donovan said. "We run 135 trains during the morning rush hour. So when there's a problem that affects that volume of trains, the potential for post-event congestion is the highest."

It was the latest in what the LIRR has reported to be increasingly common service disruptions caused by Amtrak, which owns and maintains the tunnels. Amtrak officials have attributed the increased frequency of tunnel issues to damage caused by superstorm Sandy, which inundated the underground passageways with 14 million gallons of corrosive saltwater. The agency is still looking for hundreds of millions of dollars to repair the damage.

According to the LIRR, which runs about half of all trains through the tunnels, delays caused by Amtrak rose to 1,458 incidents last year from 817 in 2012 -- an increase of nearly 80 percent.

In the first half of 2015 alone, the LIRR reported 969 Amtrak-related delays.

An Amtrak spokesman referred questions to the LIRR.

LIRR Commuter Council chairman Mark Epstein said that while the disruptions may not have been the LIRR's fault, "how they dealt with it is."

Epstein criticized the agency's communications efforts, noting that train conductors had insufficient information to pass along to customers, and that the railroad did not have representatives at key points on Long Island to help guide customers and answer their questions. Those answers, in some cases, could have made the difference between whether a commuter chose to board a train.

"We have people that have been sitting on trains for two hours. That's not a delay," Epstein said. "If people know what's going on, they're very understanding."

The LIRR "is the circulatory system of the metropolitan area," Cuomo said. "It does a fantastic job, but it needs rebuilding and it needs repair ..."

With Emily Ngo

Holly Munter Koenig of Westbury caught the 7:06 train west to Penn Station to go to work on Lexington Avenue and East 40th Street. At 8:50 a.m., her train was pulling into Jamaica station, about 45 minutes behind schedule.

"It was a good day to stay home and work," she said. "A lot of times I do. I should have today."