Manafort lied to the Federal Bureau of Investigation (FBI) and prosecutors about a payment to a law firm and his interactions with a suspected Russian operative in 2016 and 2017, Judge Amy Berman Jackson ruled.
In November, Mueller had accused Manafort of lying to prosecutors, a charge Manafort's lawyers dismissed.
Berman said she would consider the lies at a sentencing hearing on March 13.
Mueller's side is "no longer bound by its obligations under the plea agreement, including its promise to support a reduction" in Manafort's sentence, she said.
Presidential pardon?Manafort had pleaded guilty to conspiracy and witness tampering in September, but agreed to cooperate with Mueller to get a reduced sentence.
A prosecutor working as a member of Mueller's team said Manafort may have lied to increase his chances of getting a presidential pardon.
Read more: Donald Trump will be impeached in 2019, says 'prediction professor'
Mueller is leading a probe into Russian government meddling in the 2016 presidential election and has been looking into ties between Trump's campaign and Russia.
Manafort was the first person to be indicted as part of the investigation. Mueller has also charged six other people involved in the campaign.
amp/rc (dpa, AFP, Reuters, AP)
Each evening at 1830 UTC, DW's editors send out a selection of the day's hard news and quality feature journalism. You can sign up to receive it directly here.