Summer repairs at Penn Station could be especially bad for those traveling during peak hours.
MTA board members say Amtrak's weekday track work planned for this July and August will be done primarily during the morning and evening rushes.
Details are still being ironed out, but transit officials say they're hopeful to provide riders with other options for their commute.
"We are planning to make an announcement in the near future as to what the service alternatives can be for our customers." said LIRR President Pat Noawakowski.
"We're hopeful that people will at least understand this is the schedule that's going will be, this is what's going to happen on a two-month basis and not have to worry everyday about whether their train is going to run or not run," said board member Mitchell Pally.
Governor Andrew Cuomo wrote a letter to the president over the weekend, asking him to provide the state with federal funding to help repair Penn Station.
Earlier this month, he and New Jersey Governor Chris Christie suggested Amtrak cede control of the transit hub to a private owner.
This follows a series of issues at the station, including multiple derailments, which have led to delays and cancellations.