It only means that Manafort will have to answer for his alleged witness tampering in two ways, with respect to bail and at trial.
Manafort's attorneys filed their response to the initial accusations contained in the motion to revoke or revise pretrial release conditions roughly two hours before a midnight deadline on Friday night.
Prosecutors have accused Mr Kilimnik of having links to Russian intelligence.
Manafort is now out on house arrest and a $10 million unsecured bail.
The indictment charges that former Ukraine president Viktor Yanukovych and his political party retained lobbyists through Manafort to serve as intermediaries with the former European politicians. The government accuses Manafort of dodging taxes, failing to register as a foreign agent while working in Washington on behalf of foreign governments, and other charges.
According to documents posted in the electronic database of the court, Manafort and kilimnik accused of attempting to obstruct justice, perjury, conspiracy to obstruct the authorities and conspiracy to commit money laundering, reports TASS.
Manafort's filing on Friday was not responding to the obstruction of justice charges, but to an earlier request by Mueller that the judge consider putting him in detention before his trial due to the alleged witness tampering.
They said Kilimnik may have reported to Russian intelligence officers in Moscow or Kiev or both on his work at the International Republican Institute office in Moscow where he was employed for a decade to 2005 and later on his work for Manafort in Ukraine. The individuals shared communications with prosecutors, the government said.
"The special counsel creates an argument based on the thinnest of evidence", wrote the defense team led by Washington attorney Kevin Downing.
Emails show that during the middle of the campaign, Manafort told Kilimnik he was willing to provide "private briefings" about Trump's presidential run to a billionaire close to Russian President Vladimir Putin.
A judge is set to hear arguments on June 15. They said Mueller's "very public and very specious" filing was a pressure tactic on Manafort that may have "irreparably damaged" his right to a fair trial in the District of Columbia, signaling they may seek to move the case to Virginia. Manafort's lawyers would find the hard work of trial preparation even more challenging with their client in jail, Zeidenberg said.
Konstantin Kilimnik, a longtime associate of both Trump and Manafort, was also charged. "This is strong evidence of consciousness of guilt", said Zeidenberg, who prosecuted I. Lewis Scooter Libby, Vice President Dick Cheney's chief of staff. John is Manafort's middle name, and Hannah is the middle name of that of his then-business partner, Rick Davis. Gates is cooperating with prosecutors against Manafort.
The communications by Manafort were "in an effort to influence their testimony and to otherwise hide evidence", an Federal Bureau of Investigation agent Brock Domin wrote in a declaration filed to the court earlier this week.
Kilimnik attended a Soviet military school where he learned to speak fluent Swedish and English, which complemented the Russian and Ukrainian he already spoke.
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