WASHINGTON — Paul Manafort, President Donald Trump's former campaign chairman, lied to prosecutors repeatedly despite his plea deal to cooperate, but a judge allowed Justice Department special counsel Robert Mueller to file a secret document describing the breach.

U.S. District Judge Amy Berman Jackson decided Friday to allow Mueller to file the document under seal. A redacted version of the document, with a portion of the explanation, might still be filed.

Terree Bowers, a former U.S. attorney in Los Angeles now in private practice at Arent Fox, said keeping the filing under seal is part of Mueller’s classical investigative approach of starting with subordinates then moving higher up the chain of command.

“It suggests that the overwhelming majority of the document, if not all of it, is confidential information that they don’t want out at this point in the investigation,” Bowers said.

Because Manafort has a joint defense agreement with Trump, the move could also limit what is shared with the president, Bowers said.

“Given the allegations that Manafort’s lawyers have been relaying information to Trump and his lawyers, they have to be somewhat concerned about revealing various legal theories and what they have left to pursue factually,” Bowers said. “Even the exact areas where they think Manafort has lied would be invaluable for Trump and others to know at this point.”

Mueller voided the plea agreement Nov. 26 because of how Manafort tried to mislead prosecutors investigating Russian interference in the 2016 election. The shocking move lost Manafort a chance at a shorter prison term, but also cost Mueller a highly placed witness.

In revealing the collapse of the plea deal, Mueller signaled that he had learned enough during his 18-month investigation to determine that Manafort was lying. The move also served as a warning to other witnesses: Don't lie.

Mueller and his team still have the cooperation of Manafort’s top deputy, Rick Gates; Trump’s former personal lawyer, Michael Cohen, and former National Security Adviser Michael Flynn.

Prosecutors also filed an argument Friday in federal court in New York calling for Cohen to be imprisoned when he is sentenced Dec. 12 for lying to Congress and for making hush payments to women alleging they had extramarital affairs with Trump. Prosecutors are asking for no prison time for Flynn's cooperation when he is sentenced Dec. 18 for lying to the FBI about his contacts with Russians during the transition.

But Manafort was a key figure in the Russia inquiry. He was Trump's campaign manager from March until August of 2016, during a crucial part of the campaign when Trump secured the Republican nomination and the GOP held its convention in Cleveland.

Manafort came to the campaign with a history of dealing with Russians and attended the June 2016 meeting at Trump Tower during which the attendees were to discuss information promised to damage Democratic nominee Hillary Clinton.

A jury convicted Manafort of eight bank and tax charges in August for representing a pro-Russia faction in Ukraine. Sentencing in that case is scheduled Feb. 8.

But he’s also a tainted witness after pleading guilty in September to conspiring to obstruct justice, for urging other witnesses to provide inaccurate accounts to investigators while he was in custody. Sentencing in that case is March 5.

Manafort continued to have a joint defense agreement with Trump even as he said he was cooperating with Mueller. Trump, who has criticized the Mueller probe as a "witch hunt," kept open the possibility he could pardon Manafort and called him a "brave man."

As a witness, Manafort could have offered Mueller a seat inside the room at the Trump Tower meeting. He attended the meeting with the president’s son, Donald Trump Jr., son-in-law Jared Kushner and Russian lawyer Natalia Veselnitskaya.

Trump Jr. has acknowledged seeking “dirt” on Clinton but insisted he did nothing wrong. Nobody has been charged related to that meeting.