Amtrak says it needs a major construction project to move forward before it can make repairs to its tunnels beneath the East and Hudson Rivers.
In a report released Thursday, the railroad says the tunnels are safe for train operations, but that sea water from Hurricane Sandy caused significant damage to the walls and track systems.
It suggests taking individual tubes out of service for extended periods of time to make necessary repairs.
Amtrak also says it needs to be able to complete its Gateway Program, which would create a new, two-track tunnel under the Hudson.
It says that project would alleviate service disruptions when the older tunnels are shut down.
Many commuters who spoke with NY1 at Penn Station said the shut-downs would be a necessary evil.
"I'm sure it would be a big inconvenience when they do shut them down but you gotta get them repaired. Gotta be patient," said one rail rider.
"I know it has to be done but it's unfortunate that we have so few tunnels at this time," said another rail rider.
Amtrak tunnels are also used by Long Island Rail Road and New Jersey Transit, which could both face service disruptions if the tunnels are repaired.