Mr. Manafort, convicted by a Virginia jury in August on bank and tax fraud charges, was due to go on trial a second time on related charges in Washington.
On Thursday, ABC News reported that Manafort's legal team had reached a tentative deal with Mueller's team after an hours-long meeting at the special counsel's downtown Washington, DC, offices.
The charges in Friday's filing were contained a criminal information, a document which can only be filed with a defendant's consent, generally signaling an agreement has been reached.
Jurors in Virginia last month found Manafort guilty, in a separate case, on two counts of bank fraud, five counts of tax fraud and one charge of failing to disclose foreign bank accounts, giving special counsel Robert Mueller a victory in the first trial arising from his investigation of Russia's role in the 2016 USA election.
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The investigation looked at such interactions "before and during the campaign to plumb motives and opportunities to coordinate and to expose possible channels for surreptitious communications", prosecutors wrote.
The trial included testimony for the prosecution from Manafort's longtime aide, Rick Gates, who pleaded guilty to lying to federal authorities and agreed to co-operate with the special counsel probe.
The punishment that Manafort may receive related to his D.C. case, and any cooperation he may have offered the government, weren't immediately clear.
Manafort, 69, was a key figure in Mr Trump's inner circle, but the president has since sought to distance himself from his former adviser. And during his Virginia trial in August, Manafort's lawyers spent considerable time painting Gates as a liar, embezzler, philanderer and turncoat who would say anything to get a lighter prison sentence. The jury was deadlocked on the remaining 10 counts, which ended in mistrial. The three-week trial centered on income Manafort earned working as a political consultant for pro-Russian Ukraine.
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During Manafort's first trial, Judge Ellis often butted heads with federal prosecutors.
Kevin M. Downing, an attorney for Manafort, also said earlier this summer there was "no chance" his client would flip and cooperate with prosecutors.
For months, Manafort had refused to turn on his former boss, unlike other Trump administration figures.
However, none of the charges relate to collusion with Russian Federation in the election.
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This comes ten days before Manafort's trial was set to begin.