Gov. Andrew Cuomo wants Amtrak to foot a $50 million bill for the MTA’s mitigation plans during the “summer of agony” at Penn Station.

The MTA unveiled details of the Long Island Rail Road’s summer service plan on Monday as Amtrak prepares to take several tracks at Penn Station out of service between July 10 and Sept. 1. It did not, however, explain how the plans would be paid for.

“Amtrak’s emergency track repairs this summer at Penn Station will cause significant disruption to the commuters from New York and New Jersey,” Cuomo said in a statement Thursday. “The resulting question is – who pays for all of this?”

The LIRR currently pays $50 million a year – roughly $4.16 million per month – to rent the tracks at Penn Station, which are owned by Amtrak.

“As the tracks are not available due to Amtrak’s actions, they are liable for the resulting damages,” Cuomo said in the emailed statement.

The payouts to Amtrak are made monthly and, much like a tenant unhappy with building repairs refusing to pay their landlord, the state would simply not dole out future monthly payments to Amtrak, a spokeswoman with Cuomo’s office said.

Cuomo also urged the MTA board to recoup the payments already delivered to Amtrak, and threatened to introduce legislation to stop payments if the board declines to do so.

“We do not know at this time what the total cost of mitigation will be, but I believe as a matter of principle, whatever the ultimate cost, it should not be borne by the commuters or taxpayers of the State of New York,” Cuomo said.

Amtrak on Thursday defended its decision to conduct track repairs during the work week, saying they can’t be done “efficiently or promptly on nights and weekends alone.”

The railroad said that while Cuomo’s frustration is understandable, it does not agree with the assertion that Amtrak should pay.

“We all have a responsibility for taking the necessary steps to improve Penn Station and the funding that LIRR pays Amtrak for their proportional share of operating, maintenance and capital costs is required to keep the station operating reliably and safely into the future,” Amtrak said in an emailed statement. “Withholding such investments will only mean less work accomplished and more delay and impacts for riders.”

The LIRR said it expects weekday service to be reduced by about 20 percent during the eight weeks that Amtrak will make critical track repairs.

To help offset the disruptions, the LIRR said it would increase train capacity with 36 additional cars. A new ferry route between Long Island and Manhattan was also introduced, and 200 coach buses will be deployed to help shuttle commuters.

In anticipation of more cars on the road during peak hours, the state has also fast-tracked a number of bridge and tunnel projects, including a conversion to cashless tolls, so that all bridge and tunnel lanes will be open when train service is reduced.

Sen. Todd Kaminsky (D-9th District), who represents residents in southwest Nassau County, commended Cuomo for asking Amtrak to pay up.

“The governor is right to say that Amtrak should bear the cost of the additional services that the MTA must provide during the upcoming nightmarish summer when Amtrak will be closing down and repairing tracks at Penn Station,” Kaminsky said in an emailed statement. “Long Island fare payers should not be funding the costs that result from Amtrak’s years of neglect.”

Additionally, Kaminsky said he wants the MTA to use “any funds” it may get back from Amtrak to go toward fare reduction for LIRR commuters.

One glaring item missing from the MTA’s summer service plan was fare reduction for riders – something that NJ Transit has offered its commuters on lines most impacted by the Penn Station track repairs.