The head of Amtrak told the MTA on Wednesday that it will sue the agency if it fails to cough up rent money for Penn Station.

A letter sent from Amtrak CEO Wick Moorman to MTA brass on Wednesday says that they have to pay the $50 million in annual rent even if some tracks won’t be available for the Long Island Rail Road during construction this summer. The agency was hoping to stop making the payments and use the cash for ferries and buses to New York City and to give some affected riders a 25 percent discount.

But Moorman said that will take more money from the riders.

“What it will do is harm the thousands of commuter railroad passengers who pass through the station each weekday aboard nearly 600 LIRR trains and the New York City and state economies that depend upon Amtrak, the LIRR and New Jersey Transit service,” he wrote.

Gov. Cuomo directed the agency to stop paying Amtrak, but many MTA board members felt it was the wrong move.

“When you are facing a crisis, it’s the time when all the agencies need to work together,” said Polly Trottenberg, an MTA board member and head of the city’s Transportation Department.