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A federal judge in a closed hearing questioned where Paul Manafort’s loyalties lie considering that he gave false statements to investigators to shield a conspirator in a pro-Russian lobbying effort.

Judge Amy Berman Jackson in federal court in Washington, D.C., earlier this week said that because Manafort lied to investigators on three occasions, prosecutors for special counsel Robert Mueller are not bound by a prior deal to give him a lighter sentence in exchange for his cooperation.

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“To me, this is definitely an example of a situation in which the Office of Special Counsel legitimately concluded he's lying to minimize things here, he's not being forthcoming, this isn't what cooperation is supposed to be," the judge said, according to a sealed transcript of the Wednesday hearing that was released Friday night with redactions that were agreed to by prosecutors and Manafort's lawyers.

“This is a problematic attempt to shield his Russian conspirator from liability and it gives rise to legitimate questions about where his loyalties lie," Jackson said, referring to Konstantin Kilimnik.

As NBC News has previously reported, the FBI has asserted that Kilimnik has ties to Russian intelligence

"I find by a preponderance of the evidence that Mr. Manafort made intentional false statements to the FBI and the grand jury with respect to the material issue of his interactions with Kilimnik," the judge said.

In September, Manafort pleaded guilty in the U.S. District Court in Washington to conspiracy to defraud the U.S. and to witness tampering.

He agreed to cooperate with investigators, but prosecutors have since told the court that he lied to them and the deal should be called off.