Special counsel Robert Mueller has filed a court document on alleged lies told by Paul Manafort to Mueller's team in violation of the plea deal signed by the ex-Trump campaign chairman.

Here are the key takeaways:

The document laid out five key lies Manafort allegedly told the special counsel and the FBI. Those alleged lies related to suspected Russian spy Konstantin Kilimnik and a wire transfer to a firm working for Manafort, as well as "information pertinent to another Department of Justice investigation" and "Manafort's contact with Administration officials."

Large sections of the document detailing the alleged falsehoods are blacked out. The most heavily redacted portions related to Manafort's interactions with Kilimnik.

The special counsel said evidence "demonstrates that Manafort lied about his contacts" when he said after signing his plea deal that he had "no direct or indirect communications with anyone" in the Trump administration.

Manafort was talking to people in the Trump administration as late as 2018, the document alleges: "In a text message from May 26, 2018, Manafort authorized a person to speak with an Administration official on Manafort's behalf. Separately, according to another Manafort colleague, Manafort said in February 2018 that Manafort had been in communication with a senior Administration official up through February 2018."

Mueller said Manafort's lies "were not instances of mere memory lapses," and that the special counsel "is available to prove the false statements at a hearing" if Manafort challenges the most recent allegations against him.

In response to the court filing, White House Press Secretary Sarah Sanders issued the following statement:

The government's filing in Mr. Manafort's case says absolutely nothing about the President. It says even less about collusion and is devoted almost entirely to lobbying-related issues. Once again the media is trying to create a story where there isn't one.

Read the full filing here.

Before the filing was released, a federal judge ordered Mueller to file his full submission about ex-Trump campaign chairman Paul Manafort's "crimes and lies" out of public view.

U.S. District Judge Amy Berman Jackson granted Mueller's request to file under seal the "unredacted version" of the court document, in which the special counsel was expected to defend its determination that Manafort lied to investigators in violation of the terms of his plea deal.

But a version of the filing with blacked-out portions would still be released to the public, the judge ordered.

Just as the court filing was released, President Donald Trump tweeted: "Totally clears the President. Thank you!" Trump did not specify whether or not he was referring to the submission in Manafort's case.

Trump tweet

The decision from Jackson in Washington, D.C. federal court came shortly before Mueller's deadline to submit the document.

In a prior filing, the special counsel accused Manafort, 69, of lying about a "variety of subject matters" to investigators, without providing details about the allegation. His plea agreement with the special counsel required him to fully and truthfully cooperate with investigators.

In a court appearance following that allegation, attorneys for Mueller revealed that they were mulling over whether to file new charges against Manafort.

Manafort was already on the hook for a raft of criminal charges lodged by Mueller.

In August, Manafort was convicted in Virginia federal court of eight counts related to his past work on behalf of a pro-Russia political party in Ukraine. He is due to be sentenced in that case on Feb. 8.

In September, on the eve of a second trial in U.S. District Court in Washington, Manafort struck a deal with Mueller in which he pleaded guilty to two counts of conspiracy, one of which related to money earned from his work in Ukraine, the other of which was related to his effort to tamper with witnesses against him. His sentencing in that case is tentatively scheduled for March 5.

--CNBC's Jacob Pramuk and Tucker Higgins contributed to this report