Mueller's team did not spell out what Manafort lied about.
Manafort had agreed to cooperate with special counsel Robert Mueller's investigation of possible collusion between the Trump campaign and Russian Federation as part of a plea deal in September. He was convicted by a jury in August on tax and bank fraud charges in the other case in Virginia.
A month later he pleaded guilty to two other criminal charges in a plea deal with Special Counsel Robert Mueller.
He pleaded guilty in October 2017 and pledged to cooperate with the Mueller probe, and was later sentenced after expressing his remorse that he "lied in an investigation that was important to national security".
The surprise development came at a critical time for Mueller, who is expected to finalise a report in the coming months on the findings of his 18-month probe into Russia's election meddling and possible collusion between Moscow and the Trump campaign.
As part of his plea deal, Manafort admitted to committing a host of money laundering and foreign lobbying crimes and fraud, giving the federal prosecutors ample leverage over him. But special counsel prosecutors were "not getting what they want", one source with knowledge of the discussions said.
In September Manafort accepted the plea deal on related conspiracy charges in return for an agreement to co-operate with Mr Mueller's investigation.
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Both the special counsel and Mr Manafort's legal representatives asked the court to set a date for sentencing.
"After signing the plea agreement, Manafort committed federal crimes by lying to the Federal Bureau of Investigation and the Special Counsel's Office on a variety of subject matters, which constitute breaches of the agreement", prosecutors wrote.
"He believes he has provided truthful information and does not agree with the government's characterization or that he has breached the agreement", Manafort's lawyers said in the same filing.
Trump has repeatedly denied collusion of any kind.
At the very least it seems unlikely that prosecutors will request a lighter sentence in response to Mr Manafort's cooperation.
As part of his plea agreement, Manafort also agreed to forfeit five properties he owned in NY, including his apartment at Trump Tower and his sprawling estate in the Hamptons.
It was the first criminal trial arising from the justice department's investigation into alleged interference by Russian Federation in the 2016 election.