Earlier this week Mr Manafort was accused of witness tampering.
He remains charged with money laundering, illegal foreign lobbying and lying to federal officials.
Days ago Mueller sought to have Manafort be put in jail while he awaits trial because he allegedly tampered with witnesses.
Although Kilimnik denies it, Mueller's first indictment alleges that he had ties to Russian intelligence as late as 2016. He has pleaded not guilty. The special counsel's team may be hoping the prospect of pre-trail incarceration could help change Mr Manafort's mind.
Prosecutors already claimed that Manafort misled federal authorities for years about his lobbying work in the USA for Ukrainian politicians before he joined the Trump campaign.
President Donald Trump's former campaign chairman Paul Manafort on Friday was hit with a second superseding indictment by Special Counsel Robert Mueller's office charging him with obstruction of justice.
Mueller has suggested in previous filings that Kilimnik had ties to Russia's spy agencies. The skeleton for future allegations, however, can now be discerned. No charges were filed but the Ukrainian who called for the investigation seemed sure Kilimnik had links to Russian Federation.
Mr Mueller, who is investigating possible collusion between the Trump campaign and Russian Federation, has asked the judge overseeing the case in US District Court for the District of Columbia to revoke or revise an order releasing Mr Manafort ahead of his trial.
Mr Mueller was appointed after Mr Trump fired Federal Bureau of Investigation director James Comey last May.
Legal experts say Manafort's alleged efforts to convince witnesses to assert that the Hapsburg Group had only been active in Europe would have allowed Manafort to argue he had not violated FARA. It's not clear exactly what Manafort knows, but he does appear to be a linchpin between Trump's campaign and Russian Federation.
"It's far too early to be thinking about it", Mr Trump told reporters before travelling to the G7 summit in Canada.
"They haven't been convicted of anything".