(CNN) Two prominent Washington lobbying firms are in the crosshairs of the Justice Department's special counsel investigation as new details of their relationship with Paul Manafort and his deputy Rick Gates were revealed in court filings.

In the indictment of Manafort and Gates unsealed this week, the lobbying firms were described only as 'Company A' and 'Company B,' but people familiar with the lobbying activity tell CNN that special counsel Robert Mueller's team was referring to Mercury LLC and Podesta Group.

The two lobbying firms under scrutiny have said they are cooperating with Mueller's investigation into whether anyone from the Trump campaign colluded with Russians to influence the election.

A spokesman for the special counsel declined to comment.

Vin Weber, a former Republican congressman from Minnesota, led the effort for Mercury, according to the agreement filed as part of the firm's Foreign Agents Registration Act (FARA) filing. Tony Podesta, a well-known Democratic lobbyist and brother of Hillary Clinton's campaign chairman, John Podesta, was the point person for Podesta Group. Podesta, his company, Weber and Mercury have not been accused of any wrongdoing.

The special counsel investigation is looking into Podesta and Mercury's link to Manafort and Gates and whether the firms properly identified as foreign agents for work they did for the Brussels-based European Centre for a Modern Ukraine, according to people familiar with the inquiry. Under the FARA, anyone representing a foreign political party or government must publicly file reports disclosing the relationship and details of their meetings.

Lawyers knowledgeable about lobbying laws say there have been few cases against unregistered foreign agents, and some could not recall any case against a firm that filed as a lobbyist but not a foreign agent. However, the decision to charge Manafort and Gates with failing to file as foreign agents relating to a decade of work they did for the Party of Regions, a pro-Russia political party in the Ukraine, shows a willingness by the special counsel's team to pursue those types of false filing cases. Manafort and Gates both pleaded not guilty to the charges.

Manafort's attorney noted the infrequency of prosecutions when he sought to alter bail conditions.

"The U.S. Department of Justice has only brought six criminal FARA prosecutions since 1966 and it has secured only one conviction during this period," said Kevin Downing, Manafort's defense attorney. "It is far from clear what activity triggers a requirement to file a report as a foreign agent."

The Manafort and Gates indictment leaves little discretion about the special counsel's view of the ECFMU, describing it as being "under the ultimate direction of the government, the Party of Regions and its candidate Viktor Yanukovych."

The ripple effect of the charges came quickly: Tony Podesta resigned that same day, and a person familiar with Podesta Group said a new firm with a new name would be launched to salvage clients.

The role of the lobbying groups, especially Podesta, has been seized upon by some Republicans who are trying to entice the special counsel to scrutinize the activities of the Clinton campaign and the Democratic National Committee.

Podesta and Mercury fit into the Manafort case because of work they did from 2012-2014 for the ECFMU to improve the country's ties to the West. Both Mercury and Podesta say they filed multiple lobbying reports on the advice of lawyers and after receiving a written certification from the ECMFU stating that it was not "directly or indirectly supervised, directed, controlled, financed or subsidized in whole or in major part by a government of a foreign country or a foreign political party."

They did not register as foreign agents until public reports last year raised questions about the independence of the ECFMU. The filings were made to the Foreign Agents Registration unit of DOJ and signed by Podesta and Weber.

In a statement Podesta Group said, "Two and a half years after the engagement ended, the Podesta Group read in media reports that the representations made to us by the ECFMU were apparently not accurate. Immediately, the Podesta Group voluntarily contacted the FARA office to determine if an additional FARA filing was required. When the FARA office advised that we should re-file, we did so promptly. Indeed, after we submitted our disclosure, the FARA office at DOJ informed the Podesta Group that it was not the subject nor a target of an investigation."

Authorities allege that Manafort and Gates while working for the Party of Regions recruited Mercury and Podesta as lobbyists and paid them $2 million using offshore entities. Manafort and Gates allegedly sought to stay under the radar by arranging for the ECMFU to be the nominal clients of Podesta Group and Mercury, according to the indictment. The document doesn't allege that Podesta or Mercury knew the source of the payments.

The special counsel alleges in the Manafort indictment that Gates wrote to Mercury soon after it was hired in mid 2012 that it would be "representing the government of the Ukraine." By November 2012, Gates told officials with both lobbying firms that they needed to prepare a record of their past and current efforts so the "President" could be briefed by "Paul," according to court filings.

Manafort and Gates allegedly selected both US lobbying shops, but the ECFMU signed contracts with the firms without ever meeting with the principles, according to the allegations.

Gates also allegedly sent talking points to Podesta Group in August 2016 after news reports surfaced detailing Manafort's advisory work in Ukraine. The talking points sought to distance Manafort and Gates from the ECFMU's association with Podesta and Mercury, the indictment alleges.

Podesta Group "through a principal replied to Gates the same day that "there's a lot of email traffic that has you much more involved than this suggests[.] We will not disclose that but heaven knows what former employees of [Company B] or [Company A] might say," according to an excerpt included in the indictment.

The indictment alleges Manafort and Gates had weekly scheduled calls with representatives from Mercury and Podesta to provide them "directions as to specific lobbying steps that should be taken, sought and received detailed oral and written reports from these firms on the lobbying work they had performed" and also congratulated and reprimanded the lobbying firms on their work.