Judge Amy Berman Jackson, the federal judge handling the Washington case, ruled this week that Mr. Manafort had deliberately deceived prosecutors after he pleaded guilty to two conspiracy counts in September and agreed to cooperate with them in hopes of a lighter sentence. In a transcript of that hearing released Friday night, Judge Jackson said, “My concern isn’t with nonanswers or simply denials, but times he affirmatively advanced a detailed alternative story that was inconsistent with the facts.”

She found that Mr. Manafort had deceived investigators about three issues, including his dealings with Konstantin V. Kilimnik, a Russian associate who prosecutors say has ties to Russian intelligence. At one point, Judge Jackson said, Mr. Manafort’s actions seemed to constitute “an attempt to shield his Russian conspirator from liability,” adding, “it gives rise to legitimate questions about where his loyalties lie.”

Mr. Mueller’s team has been investigating whether Mr. Kilimnik played any role in Russia’s covert campaign to interfere in the 2016 presidential election. Prosecutors had told the judge that Mr. Manafort had lied about the fact that he had shared Trump campaign polling data with Mr. Kilimnik months before the 2016 election — possibly because he believed Mr. Trump would be less likely to pardon him for his crimes if his release of campaign data became known.

Defense lawyers had argued that the only real proof that Mr. Manafort ordered the data transfer came from Rick Gates, Mr. Trump’s former deputy campaign chairman, who is awaiting sentencing on charges of conspiracy and lying to federal investigators. The lawyers said that Mr. Gates was not a credible witness and that emails supposedly backing up his account were ambiguous, at best.

At the earlier hearing, Judge Jackson had questioned why Mr. Kilimnik would have been interested in polling data. Richard Westling, one of Mr. Manafort’s lawyers, maintained that some of the information, apparently the polling data, was “very detailed” and “not easily understandable.” The judge said, however, that that made Mr. Manafort’s apparent decision to share it “significant and unusual.”