The railroad said customers should take the 2 or 3 trains to Atlantic Terminal or the E train to Jamaica for service to other branches.
Service has been temporarily suspended on the main line in both directions between Penn Station and Hicksville. The accident also is affecting trains on the Port Jefferson, Ronkonkoma and Oyster Bay branches.
Floodwaters from the storm poured into Amtrak’s East River tunnels and knocked out the entire signal system that manages Amtrak and LIRR trains between Long Island and Manhattan.
While trains in and out of Penn Station are now operating with residual delays, there were major problems for getaway day commuters earlier in the day.
Modified service resumed Thursday morning after trains out of Penn Station were cancelled Wednesday night.
Some service on the eastbound Long Island Rail Road was restored, after being suspended for a second time Wednesday night.
Amtrak has announced plans to reopen three tunnels providing access to and from Penn Station on Friday, nearly two weeks after they were flooded and severely damaged by Superstorm Sandy.
Four train lines will restore service on Sunday after suffering significant amounts of damage during Hurricane Sandy.
Crews are quickly working to get rail networks back on track following the devastating toll Superstorm Sandy took on New York City Transit and parts of the Long Island Rail Road and Metro-North Railroad.
There is still no Amtrak service in or out of New York City, but the railroad is getting closer to changing that.
All subways, Metro-North and Long Island Rail Road service was suspended Sunday and it will remain that way until further notice. Bus service was also suspended.
A Midtown Direct train was headed into New York when it broke down around 8:30 a.m., officials said.
Northeast Corridor and North Jersey Coast Line trains were delayed up to 30 minutes and Midtown Direct trains were diverted to Hoboken for about an hour Tuesday.
“Whether the drug deal occurs on the street corner or on the Internet, it’s a crime,” Bridget Brennan, special narcotics prosecutor for New York City, said Thursday in a statement announcing the arrests.
Kara Alongi was found walking along the side of the Turnpike near Exit 1. She was taken to a hospital for an evaluation and reunited with her family, who have since taken her home, Clark Police Chief Alan Scherb said.
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