Manafort had been under house arrest after posting a $10M bond.
Manafort faced arraignment Friday on the obstruction counts and is set for trial in Washington in September over the allegations of secret lobbying.
While under house arrest, Manafort allegedly tried to use his former Russian fixer, Konstantin Kilimnik, to contact two witnesses in his money laundering case and persuade them not to make certain statements to investigators.
"They've gone back 12 years to find things about somebody, and I don't think it's right", he said.
The judge said sending Manafort to a cell was "an extraordinarily hard decision" but said his conduct - allegedly conspiring to contact witnesses in the case in an effort to get them to lie to investigators - left her little choice. The two witnesses were not identified in the filing.
The group's work factors into an indictment against Manafort that accuses him of acting as an unregistered foreign agent by lobbying in the USA on behalf of Ukrainian interests.
Paul Manafort departs Federal District Court after a hearing, Thursday, April 19, 2018, in Washington. He faces several felony charges - including tax evasion, bank fraud, money-laundering conspiracy and acting as an unregistered foreign agent - related to his Ukrainian political work, money he funneled through offshore accounts and loans he took out on property in the U.S. I can't take away his cellphone.
Prosecutors argued on Friday that Manafort could continue to engage in alleged criminal activity if he is not jailed.
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He had been confined to his home on electronic monitoring and other restrictions since he was first indicted October 27 during special counsel Robert Mueller III's probe of Russian interference in the 2016 presidential election.
"Didn't know Manafort was the head of the Mob", he said. Prosecutors have previously said Kilimnik has ties to Russian intelligence, which he denies.
Manafort's attorneys have accused prosecutors of conjuring a "sinister plot" out of "innocuous" contacts.
Legal experts say Mueller wants to keep applying pressure on Manafort to plead guilty and assist prosecutors as Gates did and is cooperating with the probe after cutting a plea deal.
The Manafort case focuses on his work between 2004 and 2014 in Ukraine for pro-Russia politicians including former Ukrainian president Viktor Yanukovych.
The indictment accused them of attempting to call, text and send encrypted messages starting in February to two people from a political discussion group - the so-called Hapsburg Group - that worked with Manafort to promote Ukraine´s interests in a bid to sway their testimony.
The investigation against Manafort is part of the investigation about the so-called Russian intervention in elections in the United States. The group included one unidentified former European chancellor.