Special counsel Robert Mueller files witness tampering indictment against Paul Manafort and Russian citizen Konstantin Kilimnik

• Special counsel Robert Mueller filed new witness tampering charges against ex-Trump campaign chief Paul Manafort and Russian national Konstantin Kilimnik
• Mueller was already asking a judge to revoke Manafort's $10 million bail.
• President Donald Trump has repeatedly called the special counsel's investigation into Russian interference in the 2016 presidential election a "witch hunt."

Special counsel Robert Mueller on Friday filed new witness tampering criminal charges against ex-Trump campaign chief Paul Manafort as well against Russian citizen and former Manafort operative Konstantin Kilimnik.

The superseding indictment — the third against Manafort issued by a Washington, D.C., federal grand jury — came days after Mueller asked a judge to revoke Manafort's $10 million bail and jail him because of alleged efforts to tamper with potential witnesses at his upcoming trials.

Manafort, 69, and the 48-year-old Moscow resident Kilimnik were both charged with obstructing justice and conspiracy to obstruct justice by using intimidation or force against a witness, and also with tampering with a witness, victim or informant.

The charges echo allegations Mueller made Monday in his request to revoke Manafort's bail.

Kilimnik was a longtime employee of Manafort's political consulting entities and had done work for him in Ukraine. He is also suspected of having connections to Russian intelligence services.

The indictment accuses Manafort, while being confined to his home, of conspiring with Kilimnik to influence two potential witnesses against Manafort between late February and April.

The witnesses are identified as "Persons D1 and D2" in the superseding indictment. That is exactly how Mueller, in his bail revocation request, identified two witnesses who had worked with Manafort and whom he allegedly tried to tamper with.

The "Person A" identified in Monday's filing by the special counsel as Manafort's accomplice in that effort appears to be Kilimnik.

In that filing, Mueller said that in February, after he filed a second superseding indictment against Manafort, both Manafort and Person A "repeatedly contacted Persons D1 and D2 in an effort to secure materially false testimony concerning the activities of the Hapsburg group." That group was a collection of former senior European political leaders who allegedly acted as third-party paid lobbyists for Ukraine.

Court filings say that Person D1 told Mueller's investigators that Manafort reached out to him on Feb. 26 using the WhatsApp encrypted messaging platform to say, "We should talk. I have made clear that they worked in Europe," referring to the Hapsburg group.

Person D1 told investigators he "understood Manafort's outreach to be an effort to 'suborn perjury'" because both he and Manafort knew the Hapsburg group had done work in the U.S.

Mueller's filings also cited a Feb. 28 WhatsApp message by Person A to Person D2, which said, "Basically P wants to give him a quick summary that he says to everybody (which is true) that our friends never lobbied in the US, and the purpose of the program was EU."

Person D2 turned over that message to Mueller's investigators last month.

Lobbying in the U.S. on behalf of Ukraine would have required the Hapsburg group to register with the American government, which it had not done.

Andrew Harrer | Bloomberg | Getty Images

Paul Manafort, former campaign manager for Donald Trump, arrives to the U.S. Courthouse for a bond hearing in Washington, D.C., on Monday, Nov. 6, 2017.

The superseding indictment filed by Mueller on Friday maintains five other prior criminal charges against Manafort pending in DC federal court, which relate to lobbying work he did on behalf of a pro-Russian political party in Ukraine.

Those charges include conspiracy against the United States, conspiracy to launder money, acting as an unregistered agent of a foreign principal and false statements.

Manafort is set to go on trial next month in Virginia federal court on related charges. His trial in DC federal court is set for September.

"The heat is being turned up," said Robert Ray, who served as independent counsel in the Whitewater investigation into Bill Clinton, in an email to CNBC.

"Counts Six and Seven are significant — obstruction of justice (witness tampering) and conspiracy to obstruct justice (same), alleged against both defendants and continuing through April 2018, that is, including while Manafort was released on bail," said Ray, a partner in the law firm of Thompson & Knight.

Lawyers for Manafort did not immediately respond to a request for comment. They were facing a deadline on Friday to respond to Mueller's earlier request to a judge to jail Manafort because of the alleged tampering. A hearing on Mueller's request is scheduled for June 15.

The White House had no immediate comment on the new indictment.

President Donald Trump was asked Friday if he had considered pardoning his former campaign chief Manafort or his personal lawyer Michael Cohen, who is the target of a federal criminal probe in New York City.

"It's far too early to be thinking about it," Trump told reporters. "They haven't been convicted of anything. There's nothing to pardon."

— Additional reporting by CNBC's Tucker Higgins.