Flynn is the fourth individual so far who has been closely associated with President Trump to be involved in Mueller's thorough investigation.
Mueller's spending included $3.2 million in direct and reimbursed expenditures - including more than $1.7 million for personnel, $733,000 for equipment, $362,000 for rent and utilities, $223,000 for travel and $157,000 for contract services, such as technology services and transcripts, according to the report.
The special counsel's office operates with a degree of autonomy within the Justice Department, but reports to Rosenstein regarding its budget and "certain other matters", Rosenstein said.
The expenses are from the date of Mueller's appointment, May 17, through September 30, the end of the federal government's fiscal year.
Mueller incorporated several active investigations within the Justice Department including those of Trump campaign contacts with Russian Federation, former Trump campaign chairman Paul Manafort's business activities and former national security adviser Michael Flynn. Another $220,000 helped the special counsel's office employees relocate to work with Mueller.
The office also spent almost $734,000 on equipment and about $363,000 on rent, communications and utilities.
The figures were revealed in a Justice Department report released Tuesday. Starr's sprawling investigation, which led the House to impeach Clinton for perjury, contributed to Congress letting a law that gave special investigators wide independence expire in 1999.
A campaign aide, George Papadopoulos, has also pleaded guilty to lying to investigators and is cooperating with Mueller's team.
Mueller has issued indictments or received guilty pleas from four former Trump campaign associates.
In addition, Manafort and his longtime business associate, Rick Gates, are now facing several felony charges brought by the special counsel's office. Both men admitted to lying to the Federal Bureau of Investigation about their contacts with Russians related to their work for Trump.
Last week, former national security adviser Michael Flynn pleaded guilty to lying to Federal Bureau of Investigation agents. That represents new money coming from an indefinite appropriation for independent counsels, which the Justice Department determined could be used to fund Mueller's work.