Mr. Mueller’s team has left open the possibility that it could file new charges of lying against Mr. Manafort. His lawyers say he believes he was honest during his interviews with the special counsel’s office.

The new documents were signed by Andrew Weissmann, a prosecutor known for his no-holds-barred approach who has become a favorite target of President Trump’s. “He wrongly destroyed people’s lives,” Mr. Trump declared of Mr. Weissmann earlier Friday on Twitter.

The filing capped a busy week for Mr. Mueller’s team. His office also filed a recommendation on Friday for the sentencing of Michael D. Cohen, Mr. Trump’s former lawyer, alongside a scathing attack from prosecutors in Manhattan who rejected Mr. Cohen’s request to avoid a prison term and accused him of using his power and influence “for deceptive ends.”

The prosecutors sought about four years in prison for Mr. Cohen when he is sentenced next week for lying to Congress about the extent of Mr. Trump’s business dealings in Moscow, as well as for campaign finance violations and other charges.

Convicted by a Northern Virginia jury in August of eight counts of financial fraud, Mr. Manafort agreed to a plea deal on the verge of a second trial. He met with the special counsel’s office at least a dozen times before they declared that he had violated the plea agreement.

Prosecutors have previously accused the Russian they say Mr. Manafort was in touch with, Konstantin V. Kilimnik, of ties to Russian intelligence. A Russian Army-trained linguist, Mr. Kilimnik served as Mr. Manafort’s right-hand man in Ukraine for more than a decade, working on behalf of the country’s Russia-aligned former president, Viktor F. Yanukovych, his party and the oligarchs behind it.

In Friday’s filing, prosecutors blacked out much of the information related to Mr. Kilimnik but revealed that some of it had been uncovered in emails and testimony. They claimed that Mr. Manafort lied about various interactions and meetings with him, as well as about his involvement with witnesses who might testify against Mr. Manafort.