The Metropolitan Transportation Authority says Metro-North's Port Jervis line suffered "catastrophic'' damage from Tropical Storm Irene.
The agency says it may take months to repair large sections of track, reports the New York Post.
MTA Chairman Jay Walder toured the damaged areas on Wednesday.
He said that there are sections of track suspended in the area. He said the foundation, tracks and signals will have to be rebuilt in many sections.
Passengers on the Port Jervis line are being accommodated on buses. The line runs from Port Jervis to Suffern, where trains continue to Hoboken along NJ Transit tracks.
NJ Transit was mostly operating on a normal schedule by Thursday, with limited detours on the Raritan Valley line through Bound Brook.
The Long Island Rail Road restored service between Ronkonkoma and Greenport in time for Thursday's morning rush. LIRR will be providing full service on all 11 branches Thursday morning for the first time since Hurricane Irene struck when it restores service between Ronkonkoma and Greenport.