Mr Mueller is leading the investigation into Russian interference in the 2016 US Presidential election, and possible collusion from the Trump campaign. In August Mr Manafort was convicted of a range of financial crimes. He went on to cut a deal with prosecutors, under which he pleaded guilty to charges of witness tampering and conspiracy.
However on Wednesday Judge Amy Berman Jackson found Mr Mueller “intentionally” lied, breaking the terms of the deal and thus voiding it.
Judge Jackson claimed Mr Manafort “made multiple false statements to the FBI, the Special Counsel’s Office and the grand jury concerning matters that were material to the investigation”.
She explained he lied about money he received for legal bills, his dealings with Russian associate Konstantin Kilimnik and a separate Justice Department criminal investigation.
However on two other counts he was exonerated of having intentionally lied.
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Mr Manafort is still bound by the deal he struck, meaning he is unable to reverse his ‘guilty’ pleas.
However Mr Mueller’s office is no longer required to ask for a reduced sentence, as had been agreed under the deal.
On August 2, 2016, Mr Manafort met Mr Kilimnik, and there is a dispute over whether they discussed moves which could reduce US sanctions on Russia.
Trump appointed Mr Manafort as his campaign director in June 2016.
He resigned two months later in August, after allegations about his Russian connections emerged.
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Previously Mr Manafort had advised Viktor Yanukovych, the pro-Russian President of Ukraine who was overthrown in 2014, between 2004 and 2010.
Mr Manafort, who has already spent eight months in prison, will be sentenced on March 13.
He potentially faces decades in prison, with two separate sentences for the financial convictions and his guilty plea.
Mr Manafort outside a Washington DC courthouse in May last year