An internal legal memo that the U.S. attorney's office says was filed by mistake reveals that federal lawyers believe it will be difficult for the government to win its case against congestion pricing.

The letter, dated April 11, was uploaded to PACER, the electronic filing system for the federal courts, by a U.S. attorney defending Transportation Secretary Sean Duffy in the suit brought by the MTA against him.

The letter is addressed to the lead litigator at the federal DOT and says that it “is very unlikely that Judge Liman or further courts of review will uphold the Secretary’s decision on the legal grounds articulated in the letter.”

However, the letter offers an alternative argument that the Federal Highway Administration “may be able to accomplish the same goal, for the same reasons, utilizing established OMB procedures for the termination of cooperative agreements."

Columbia Law School Professor Michael Gerrard says that may not apply, and even if it did, it could be a lengthy process, taking months or even years, and end up in the MTA’s favor.

“There are certain procedures like hearings they have to follow, and very importantly, as acknowledged by the letter, would have to undergo its own environmental review process. Shutting down congestion pricing would have its own environmental impact,” he said.

The U.S. Attorney's office for the Southern District of New York issued a statement on the letter that reads, in part: "This was an honest error and was not intentional in any way. Upon realizing the error, we immediately took steps to have the document removed. We look forward to continuing to vigorously advocate in the best interest of our clients."

A federal Department of Transportation spokesperson said handling of the federal case is being moved from SDNY to the civil division of the Department of Justice.

In a statement, the USDOT spokesperson said SDNY's posting of the letter was, at the very least, "legal malpractice," and said it was "sad to see a premier legal organization continue to fall into such disgrace."

"SDNY's memo doesn't represent reality. Kathy Hochul's congestion pricing war against the working class was hastily approved by the Biden Administration after Donald Trump was elected," the statement said, in part.

Duffy has sent three letters to the MTA and Gov. Kathy Hochul saying that congestion pricing is not allowed under what's called the Value Pricing Pilot Program because there's no free alternative, among other arguments.

Speaking on the Brian Lehrer show Thursday on WNYC, MTA Chair and CEO Janno Lieber would not comment on the letter specifically.

"We have always been absolutely confident that congestion pricing could not be taken down unilaterally by the federal government, that they're not entitled to terminate the program under the terms of the federal Value Pricing Program, which is what it's called, or just basic legal realities,” Lieber said.

While several other lawsuits against the program were dismissed last week, there are still a few outstanding, including one from Long Island state Assemblymember Jake Blumencranz, whose suit is based on Duffy’s initial letter. He says this memo doesn’t affect his case.

“I don’t think the opinions of these three attorneys on the pros and cons of the case change the facts for us in our case, which is, and they reiterate, that a letter is operative, that tells the MTA and the State of New York that they cannot continue this program if there’s not a partnership between the federal government and the State of New York,” Blumencranz, a Republican, said.

Duffy sent a letter earlier this week giving a May 21 deadline to either shut off the tolls or give a reason why they were legal, or he’d pull federal funding for projects.

On Wednesday, the MTA’s lawyer sent a letter to Judge Liman asking for a briefing schedule to file a preliminary injunction to prevent the funds from being withheld.