US District Court Judge Amy Berman Jackson ruled that Manafort "made multiple false statements" to the FBI, Mr Mueller's office and a grand jury.
Mr Mueller leads a probe into Russian meddling in the 2016 US election.
Manafort has pleaded guilty to some charges, avoiding a separate trial.
He was convicted of financial fraud in August, relating to his work as a political consultant in Ukraine.
He then accepted a plea deal on other charges in return for co-operating with Mr Mueller's investigation.
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