A federal judge on Wednesday found that Paul Manafort, President Trump's former campaign manager, "intentionally" lied to Special Counsel Robert Mueller in response to some, but not all, of their inquiries -- a ruling that voids his plea deal and exposes Manafort, at a minimum, to a harsher sentence.

In her decision, U.S. District Judge Amy Berman Jackson pointedly rejected some of the claims by Mueller's team, while noting that legally, prosecutors were entitled to deference on the question of whether Manafort breached the terms of his plea deal as long as they made the claim in "good faith."

Manafort, 69 seemingly avoided a second trial in Washington, D.C., before Jackson last year by agreeing to cooperate with investigators and pleading guilty to two felony conspiracy charges related to his overseas lobbying work. Prosecutors, in turn, agreed to recommend he receive a reduced sentence.

Manafort has denied intentionally misleading Mueller's team during the approximately 50 hours of interviews with investigators that he participated in following his plea deal, and said he is under stress and physically ill.

"The Office of Special Counsel (OSC) made its determination that the defendant made false statements and thereby breached the plea agreement in good faith," Jackson wrote. "Therefore, the Office of Special Counsel is no longer bound by its obligations under the plea agreement, including its promise to support a reduction of the offense level in the calculation of the U.S. Sentencing Guidelines for acceptance of responsibility."

Jackson's ruling proceeded to respond point-by-point to Mueller's allegations against Manafort to assess whether he had, in fact, breached the plea agreement -- and, in some cases, Jackson rejected the special counsel's contentions as unfounded.

Special Counsel Robert Mueller alleged that Manafort breached the terms of his plea agreement last year. (Getty and AP)

For example, Jackson wrote: "OSC has failed to establish by a preponderance of the evidence that on October 16, 2018, defendant intentionally made a false statement concerning his contacts with the administration."

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The preponderance of evidence standard is among the lowest possible standards, and meeting it would require only a showing by prosecutors that it is more likely than not that Manafort lied. Toward the end of a contentious hearing last week, Jackson took particular umbrage at prosecutors' contentions that Manafort had lied about his contacts with the Trump administration.

"And of all of them, this is the one where I have the most difficulty figuring out where the real contradiction is of moment to the investigation," Jackson said.

At that point, a member of Mueller's team replied that Manafort had lied by denying having any direct or "indirect" contacts with the administration -- and that the "indirect" statement was a lie.

Also in her ruling Wednesday, Jackson found that "OSC has failed to establish by a preponderance of the evidence that on October 16, 2018, defendant intentionally made false statements concerning Kilimnik’s role in the obstruction of justice conspiracy" to tamper with witnesses in the Russia probe.

That was a reference to Russian-Ukrainian political consultant Konstantin Kilimnik, who has ties to Russian intelligence. Prosecutors said Manafort made false statements about sharing polling data during the 2016 presidential election with Kilimnik.

Jackson held separately: "OSC has established by a preponderance of the evidence that the defendant intentionally made multiple false statements to the FBI, the OSC, and the grand jury concerning matters that were material to the investigation: his interactions and communications with Kilimnik."

Top Mueller deputy Andrew Weissmann told Jackson that Manafort's connection to Kilimnik -- whose Aug. 2, 2016, meeting with Manafort at the Grand Havana Club cigar bar in New York is under particular scrutiny -- "goes, I think, very much to the heart of what the Special Counsel's Office is investigating. ... In [August] 2016 there is an in-person meeting with someone who ... is understood by the FBI, assessed to be -- have a relationship with Russian intelligence."

The meeting occurred while Manafort was still in a high-ranking role in the Trump campaign. Rick Gates, Manafort's longtime deputy and also a Trump campaign aide, attended. And prosecutors say the three men left separately so as not to draw attention to their meeting.

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Kevin Downing, Paul Manafort's defense attorney, right, walks to the entrance of federal court on Wednesday, Feb. 13, 2019 in Washington. At left is attorney Tim Wang, another member of the defense team for Manafort. (AP Photo/Kevin Wolf)

Additionally, Jackson found by a preponderance of evidence that Manafort had lied about a wire transfer sent in 2017 to a firm by a political action committee that spent millions to help Trump's candidacy.

"OSC has established by a preponderance of the evidence that defendant
intentionally made false statements to the FBI, the OSC, and the grand jury
concerning the payment by Firm A to the law firm, a matter that was material to the investigation," Jackson wrote.

Jackson told Manafort's lawyers last week she wasn't entirely convinced by their argument that his "succession of inconsistent explanations" about the wire transfer could be chalked up to confusion caused by accounting practices.

The judge specifically ruled that the lies regarding Kilimnik and the wire transfer were "material to the investigation," as prosecutors had claimed.

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Additionally, Jackson ruled that "OSC has established by a preponderance of the evidence that on October 5, 2018, the defendant intentionally made false statements that were material to another DOJ investigation." It was not immediately clear what investigation was implicated.

Jackson said the precise impact on Manafort's upcoming sentencing on two felony charges related to his Ukrainian lobbying work, set for March 13, will be determined at a later date. It appeared unlikely Manafort would face new charges as a result of Jackson's ruling Wednesday, but it remained possible.

Manafort faces up to ten years in prison in the separate case in Virginia, where he was convicted on tax and fraud charges.

Fox News' Jake Gibson contributed to this report.