Gov. Andrew M. Cuomo on Friday doubled down on his call for the MTA to withhold Penn Station rent payments to Amtrak, saying that, even without the planned track outages this summer, the Long Island Rail Road has not been getting what it’s paying for in the dilapidated train terminal.

Also Friday, Cuomo announced further progress on the planned transformation of the Farley Post Office across from Penn into the new Moynihan Station.

Cuomo on Thursday had urged the Metropolitan Transportation Authority, the LIRR’s parent, to withhold rent payments to its Penn landlord as a means to cover the cost of the LIRR’s plan to address the reduced capacity this summer. Amtrak will be taking three tracks out of service at the rail hub for most of July and August to make infrastructure improvements.

The LIRR’s plan includes running additional trains outside of the rush hours and supplementing train service with express buses and ferries. The MTA is also incurring costs by expediting construction work at its bridges and tunnels to finish before the July 10 start of the LIRR service disruptions.

“I think, frankly, it’s unreasonable for them to ask us to pay for tracks that they’re not making available,” said Cuomo, who added that, even when it does have full use of its tracks at Penn, the LIRR should not be paying what it does because the conditions there “are so deplorable.

“I’m paying rent to use the tracks at Penn Station and you’re giving me the catacombs,” Cuomo said.

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Cuomo has said that the MTA’s rent payments total about $50 million a year. In fact, relatively little of what the MTA pays to Amtrak annually is for renting space at Penn. Under a 99-year lease dating back about 30 years, the LIRR pays Amtrak $400,000 annually for its space at Penn Station.

Under federal law, the LIRR will also pay about $27 million in operating costs and $18 million in capital costs this year, according to Amtrak.

Appearing on the Brian Lehrer Show on WNYC radio, Amtrak President Charles “Wick” Moorman said Friday that the MTA’s payments to Amtrak are primarily their share of the cost of running Penn Station. Moorman said that while Amtrak carries the fewest passengers through Penn—and the LIRR carries the most—Amtrak has paid about 70 percent of Penn’s capital costs over the last decade.

“The last thing anybody needs to do now is say, ‘Well, let’s just take money out of the station and not continue to invest,” Moorman said.

Cuomo’s comments came as he announced that the state had closed on a $1.6 billion agreement to advance work on the second phase of the Moynihan Station project, transforming the Farley Post Office into a 300,000-square-foot train hall to be shared by the LIRR and Amtrak. The project is funded by private developers, the state, the Port Authority, Amtrak and the MTA.

The first phase of the project—a bright and modern new customer concourse just west of Penn—opened Thursday. Work is scheduled to wrap up in 2020.