NEW YORK — MTA Chairman Janno Lieber blasted President Donald Trump’s Penn Station Czar Andy Byford over the plans for a rebuilt and renewed Penn Station over what he called a “simply bizarre” process to rebuild the facility that is tainted with “the appearance of impropriety.”

Lieber, whose Long Island Rail Road is the primary tenant of the Amtrak-owned train station, raised questions in a letter to Byford about the cost of the project, the process by which the feds selected a contractor and the relationship between Trump and MSG owner James Dolan. Trump watched game 3 of the Knicks championship run from Dolan’s box at the Garden.

The back-and-forth began Monday morning, when Byford sent a letter to Lieber asking the transit boss to sign on to a memorandum of agreement to participate in the design process. The MTA, whose leadership on the Penn development project was taken over by the feds, has declined to sign on for months.

“I invite you again to sign the MOA and to be fully involved, via an MOA that is built around the same agreement Amtrak signed when MTA was in charge of the project, just a few years ago,” Byford wrote.

In his Monday night response, Lieber said he received the letter only after reading about it in the press, implying it had been leaked.

“News flash,” he wrote to Byford, “that’s not partnership, that’s just gamesmanship.”

Byford and Lieber have a long working history, with Lieber serving as the MTA’s head of development during Byford’s tenure as president of New York City Transit. Despite long-rumored friction between the two transit pros, Byford and Lieber have both professed to have a good working relationship ever since Byford was announced at Trump’s pick for the Penn project in May 2025.

But none of that was on display in the exchange, which could fuel distrust between Amtrak and the MTA and potentially throw a wrench in the works.

“There’s no point in rebutting all the blah-blah about the Memorandum of Agreement you are insisting the MTA sign as a precondition of participation in the project,” Lieber wrote, before going on to say that signing the agreement would potentially alter the MTA’s ongoing lease at Penn Station, which is set to expire in 2186.

Byford, for his part, had written to Lieber that “(t)he MOA is a completely stand-alone agreement and does not water down your lease as some have incorrectly speculated.”

But Lieber went on to question key components of the feds’ plan to revamp the station.

As previously reported, Amtrak named a joint venture of Halmar and Skanska as the master developer of a public-private partnership earlier this year, following a non-public selection process. The MTA chair raised concerns of impropriety in that process, and asked how the government expected to fund its planned overhaul of the station.

Lieber specifically cited a meeting between Trump and Dolan, who owns Madison Square Garden, the massive sporting complex perched atop Penn Station. As previously reported by the Daily News, that meeting — about which Trump spoke openly with the New York Post — took place a month before the feds announced the winning proposal would be one that would not require MSG to move.

“The President reportedly met with bidders and with (MSG owner) Jim Dolan during the procurement process,” Lieber wrote. “Did those discussions further taint Amtrak’s secret developer selection process?”

Lieber also noted the president, along with Transportation Secretary Sean Duffy, met with Dolan in a skybox at MSG during the NBA Finals.

“What exactly was discussed in those encounters,” Lieber asked.

Throughout the process, Byford has characterized Trump as very personally invested in the success of the project.

The MTA boss also raised questions about the cost of the project going forward.

“Your chosen development team has been touting a version of this project for years,” Lieber wrote — a reference to a similar plan hawked by Halmar’s parent company, ASTM, prior to the federal takeover of the project — “but no one has ever seen a real professional cost estimate.”

“I have never seen a project go this far without any accounting of how it is being paid for,” Lieber continued.

As previously reported by the Daily News, Byford has publicly estimated the cost of the project to be between $7 billion and $8 billion. Where that money will come from, Byford has admitted, is still being worked out.

Federal grants and money generated through a value-capture plan have been floated as the primary funding sources. Byford has also expressed hope that Albany will decide to pony up additional cash — though Gov. Hochul has rejected that notion since the feds took the project out of the MTA’s hands in 2025.

“Perhaps there are good answers to all these questions,” Lieber wrote. “Perhaps we are faced with only the appearance of impropriety.

“But in the current environment, it can hardly be surprising that we have chosen to proceed cautiously,” he wrote.

In response, Amtrak spokesman Jason Abrams reiterated the federal railroad’s hope that the MTA would sign on to the agreement to participate in the ongoing design process

“Our letter speaks for itself,” Abrams said in a statement. “We are committed to improving the entirety of Penn Station for New Yorkers, and it’s unfortunate MTA does not seem to share that approach.”

“We will continue to act in good faith and keep the invitation open to be collaborative partners so they can provide an even better experience for their customers,” he said.

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