Manafort, 69, now loses the relative freedom he enjoyed while preparing for two criminal trials.
In a June 15 tweet following the judge's decision to revoke Manafort's bail, Trump called the ruling "very unfair".
Manafort's already been charged in a series of indictments by Mueller on counts ranging from money laundering and bank fraud to tax evasion and failing to register as a foreign agent.
Trump told reporters Friday - before the announcement of Manafort's incarceration that "Manafort has nothing to do with our campaign", and that he only "worked for me for a very short period of time".
'This is not middle school.
He pleaded not guilty on those charges and had been on home confinement in Virginia, required to wear an electronic monitoring device.
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Comey also wrote an opinion piece in The New York Times responding to the report's findings. The report found the decision not to prosecute was proper.
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But the president also stuck up for him, suggesting that Manafort's alleged crimes are too old to prosecute.
At an impromptu press conference outside the White House the president also weighed in on a new report by the Inspector General's office, which blasted the FBI's handling of the Hillary Clinton investigation, dismissing the report's conclusion that former FBI Director James Comey was not politically motivated in his actions. The two witnesses were not identified in the filing.
Manafort will learn whether he must await trial in prison or can remain on house arrest following allegations that he tried to obstruct the Russian Federation inquiry. "I can't take away his cellphone", she said. Prosecutors have previously said Kilimnik has ties to Russian intelligence, which he denies. They filed a memo written by one of the witnesses for Manafort that his attorneys say shows the work of the group, known as the Hapsburg group, was European-focused.
US District Judge Amy Berman Jackson in Washington D.C. revoked Manafort's bail which had permitted him to live in his Alexandria, Virginia, apartment under house arrest, reported CNN.
Manafort has repeatedly declared his intention to fight the charges in both jurisdictions, with his lawyers saying that he is being wrongly prosecuted for financial activities that have nothing to do with collusion to affect the election. Four days later, a grand jury indicted Manafort anew, accusing him and an associate of witness tampering.
His trial in Alexandria, the U.S. state of Virginia, on bank fraud charges is set in July, and a separate one in Washington, DC, for him on charges of money laundering and fraud conspiracy is scheduled for September.
Mueller insists Manafort's case falls within his jurisdiction because of his connection with both the Trump campaign and to officials in Russian Federation and Ukraine.