Manafort, who has been a focus of Mueller's investigation into Russia's role in the 2016 U.S. presidential election, pleaded not guilty to the charges on Friday before U.S. District Judge Amy Berman Jackson in Washington.
But the judge revoked Manafort's bail conditions, sending him to jail.
Manafort has been indicted by Mueller in both Washington and Virginia on a raft of charges, including conspiracy against the United States. His trial in the Washington case is scheduled for September.
Manafort's trial on the related charges in Virginia is set for July 25. He has pleaded not guilty to all charges.
Manafort is currently confined to his home in the Washington suburb of Alexandria, Virginia, and forced to wear a GPS monitoring device.
Mueller, whose investigation has overshadowed Trump's presidency, is investigating whether the president's 2016 campaign colluded with Moscow and whether Trump has unlawfully sought to obstruct the Russia probe. Trump has called Mueller's investigation a witch hunt and has denied wrongdoing.
Jackson had previously rebuffed Manafort's repeated requests to end his home confinement in exchange for pledging $10 million in real estate as collateral.
The indictment accused Manafort and Kilimnik of attempting to call, text and send encrypted messages in February to two people from a political discussion group - the so-called Hapsburg Group - that Manafort worked with to promote Ukraine's interests in a bid to sway their testimony.
Mueller's team this month asked the judge to revoke Manafort's bail, saying his "obstructive" conduct "instills little confidence that restrictions short of detention will assure Manafort's compliance with the court's orders and prevent him from committing further crimes."
Manafort has long-standing ties to a pro-Russian political party in Ukraine and a Russian oligarch close to the Kremlin.
The charges against Manafort in Washington include conspiracy to launder money, conspiracy to defraud the United States and failing to register as a foreign agent for the pro-Russia Ukrainian government under former President Viktor Yanukovych.
None of the charges against make reference to alleged Russian interference in the election nor the accusations of collusion between Moscow and Trump's campaign. The Kremlin has denied meddling in the election.
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