Amtrak sent a warning Wednesday that Long Island Rail Road riders would be the ones paying the price if the MTA withholds funds to Amtrak because of this summer's track repairs at Penn Station.

The MTA board met today, one day after the LIRR announced it will reduce fares an average of 25 percent for riders forced to take diverted trains. 

While at the meeting, officials with the MTA received a letter sent by Amtrak in response to public threats from Gov. Andrew Cuomo and the MTA to withhold rent payments.

"Amtrak believes such action is in clear violation of our agreements with LIRR and that the LIRR has no basis to seek compensation for such costs from Amtrak," the letter reads. 

Amtrak currently owns and operates Penn Station.

Last week, the MTA unveiled its plan to account for the repair work in July and August, which will force 20 percent of peak LIRR trains to be canceled both into and out of Penn Station. It includes express buses from eight park-and-ride locations on Long Island and a ferry service from Glen Cove to the East Side.

In the letter, it says the MTA shouldn't recover these costs from Amtrak. 

MTA board members say the only way they can cover the cost of the planned increased services this summer is by reducing some of those services or raising fares.