He has pleaded not guilty to all counts, and is expected to go on trial in Washington, D.C., on September 17.
The allegations of witness tampering relate to Manafort's criminal case in Washington where he faces charges of money-laundering conspiracy, false statements and acting as an unregistered foreign agent for Ukrainian interests.
Manafort's lawyers responded to those allegations in a sharply worded filing late Friday, accusing Mueller of contriving "dubious allegations" of witness tampering and, in so doing, poisoning the jury pool ahead of his trials.
Manafort's spokesman Jason Maloni said on Friday he was reviewing the new charges. He's awaiting trial in federal courts in Washington and Alexandria, Virginia.
Still, the new counts could make it harder for Manafort to avoid jail before he goes on trial for alleged financial crimes that largely predate his time on the Trump campaign.
Earlier this week, Trump tweeted that Manafort "came into the campaign very late and was with us for a short period of time".
Jose Luis Magana AP FILE
The filing also barred Mueller from revoking or revising the conditions of Manafort's pretrial release from prison.
The indictment, filed by Mueller in District of Columbia federal court, added Konstantin Kilimnik as a defendant and charged both men with obstructing justice in their attempts to tamper with witnesses about their lobbying work for Ukraine.
Mueller has accused Manafort of attempting to call, text and send encrypted messages in February to two people from "The Hapsburg Group", a political discussion group he allegedly worked with to promote the interests of Ukraine, in an effort to influence their testimony or hide evidence in the case.
Parts of the report that have surfaced in the media claim that Comey was "insubordinate" and faulted him for ignoring the DOJ's objections when he informed Congress in a letter weeks before the 2016 election that he was reopening the investigation into Clinton's emails.
Manafort allegedly sent one of the executives a text that said: "We should talk". After Yanukovych was elected president in 2010, Manafort reportedly stayed on as an adviser and worked on other projects in Eastern Europe, including the Party of Regions political party. Kilimnik, who prosecutors say lives in Moscow, was not in US custody Friday.
Manafort's attorneys countered that prosecutors presented "scant proof" - mostly "irrelevant, innocuous" texts, and one completed phone call of five attempts that lasted one minute and 24 seconds.
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They argue the limited amount of communications "cannot be fairly read, either factually or legally, to reflect an intent to corruptly influence a trial witness".
Manafort lawyers said even the messages cited by prosecutors "are entirely consistent with Mr. Manafort's stated position and repeated assertion of his innocence", that his lobbying was "European-focused" and that he had no idea the two recipients would be called as witnesses.
Mueller also accused Manafort of secretly paying former European politicians to lobby on behalf of Ukraine. He is now on house arrest at his condo in Alexandria, Virginia, and has a $10 million unsecured bail.
Manafort, who was chairman of Trump's campaign for several months in 2016, has been charged with multiple counts of tax evasion, money laundering and bank fraud. He has pleaded not guilty.
Prosecutors have used superseding indictments before to add new charges on Manafort.
The two witnesses reportedly told the Federal Bureau of Investigation they believed Manafort and Kilimnik had been trying to get them to lie about their work.
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Kilimnik, a Russian intelligence asset, is now under the protection of Moscow and unlikely to ever see an American court room. In some of those earlier filings, Mueller made references to a Manafort associate in Ukraine with ties to Russian intelligence. Kilimnik has denied such ties and characterized himself as "a random casualty because of my proximity to" Manafort.
Years after his work for Yanukovych ended, Manafort joined the campaign of then-candidate Donald Trump in March 2016 and served briefly as the campaign manager from June to August that year.
Asked on Friday if he would pardon Manafort, Trump refused to answer.
Manafort hired Kilimnik, who is a Russian national, as a translator in his office in Kiev, the Ukrainian capital, in 2005.
The two remained close while Manafort was working for Trump's campaign.
Deripaska has denied accepting the offer or receiving any such briefings.
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