The seven-page later, obtained by Axios, says: "We understand that the Special Counsel's Office has subsequently made extensive use of the materials it obtained from the GSA, including materials that are susceptible to privilege claims".
Several high-level Trump advisers sometimes used other email accounts to communicate about transition issues between election day and the inauguration.
According to the letter, the Mueller investigation requested, in a pair of August letters, "the emails, laptops, cell phones, and other materials" for nine transition team members working on "national security and policy matters" and four other "senior" transition team members.
The Trump team's accusation adds to the growing friction between the president's supporters and Mueller's office as it investigates whether Russian Federation interfered in the election and if Trump or anyone on his team colluded with Moscow.
A spokesman for the Special Counsel's Office declined to comment.
The GSA and officials at the special counsel's office did not immediately respond to a request for comment.
Trump himself has loudly declared Mueller's effort a waste of time. That has been proven, ' Trump told reporters on Friday. "He wants to shut down these investigations, and he wants to fire special counsel Mueller". Kory Langhofer, general counsel for the transition group, wrote to the Republican chairmen of the House Oversight committee and the Senate Homeland Security committee about what the transition contends was an "unauthorized" disclosure of its emails.
The transition lawyer is asking the members of Congress to act to protect future presidential transitions from having "private records misappropriated by government agencies, particularly in the context of sensitive investigations intersecting with political motives".
A transition attorney sent letters Saturday to two congressional committees saying the General Services Administration had improperly provided the transition records to Mueller's investigators.
The letter also makes a specific claim about communication between the government and the campaign - that Richard Beckler, then the general counsel of the GSA, "acknowledged unequivocally to [the Trump campaign's] legal counsel" in a June 15 discussion that the Trump campaign "owned and controlled" emails, and that "any requests for the production of PTT records would therefore be routed to legal counsel for [the Trump campaign]".
Among those officials was former National Security Adviser Michael Flynn, who pleaded guilty to charges of lying to Federal Bureau of Investigation (FBI) agents about his contacts with Russian officials earlier this month.
Langhofer, the Trump transition team lawyer, wrote in his letter that the GSA's transfer of materials was discovered on December 12 and 13.
Democratic Rep. Jackie SpeierKaren (Jackie) Lorraine Jacqueline SpeierHouse Democrat slams Donald Trump Jr. for "serious case of amnesia" after testimony Elaine Chao: Women can't let harassment hold them back GOP lawmaker says he'll repay cost of harassment settlement MORE (Calif.) told a local news station on Friday that a "rumor" on the Hill indicated that Trump was preparing to fire the special counsel as soon as this week.