Mueller reports to Deputy Attorney General Rod Rosenstein, who appointed him, although the rule gives a special counsel broad discretion to run the investigation without regularly consulting with the department or requesting its approval.
In addition, the department said that its various offices have also spent another $3.5 million to help assist the probe, though those expenditures would have occurred "irrespective of the existence of the" special counsel's office.
The price tag is likely to rile Republicans who have been critical of Mueller's team and wary of a lengthy and costly investigation, though independent counsels have in the past spent tens of millions of dollars on lengthy probes.
The office also spent almost $734,000 on equipment and about $363,000 on rent, communications and utilities.
The money was spent between mid-May, when the investigation began, and September 30 of this year.
The special counsel's budget itself has not been made public.
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Since then, special counsels have been governed by a Justice Department regulation.
The Whitewater investigation, which lasted much longer, was more costly. Starr's predecessor, Robert Fiske, spent an additional $6 million investigating the Clintons' involvement in the Whitewater real estate deal, according to a May 1999 GAO report.
Mueller has issued indictments or received guilty pleas from four former Trump campaign associates.
Manafort was charged, along with his longtime business partner Rick Gates, for work on behalf of Ukraine unrelated to the campaign.
Mueller also splashed out $733,969 to acquire office equipment for the investigation, which the DOJ report explained will remain federal government property after the probe is finished.
A day later, the DOJ announced that former Trump campaign aide George Papadopoulos pleaded guilty to lying to federal agents during the investigation about his contacts with three individuals said to have had connections to the Russian government.