The U.S. Justice Department's inspector general's investigation concluded Holder was unaware of the tactics until learning of them from Congress.
The 471-page inspector general's report came after an 18-month investigation, and recommends more than a dozen agency officials receive disciplinary action, The Hill newspaper reported.
Fox News reported the investigation into the anti-gunrunning program accused some officials of having a "disregard" for public safety. At least two Justice Department officials have resigned.
Under the program, the Bureau of Alcohol, Tobacco, Firearms and Explosives tried to stem the flow of U.S. guns into Mexico by purposely allowing firearms dealers to sell weapons, then tracking the guns in Mexico to drug cartel leaders.
One of the guns in the program may have been used to kill Border Patrol Agent Brian Terry.
"I have reviewed the Office of the Inspector General's report on Operation Fast and Furious," Holder said in a statement, "and the key conclusions are consistent with what I, and other Justice Department officials, have said for many months now: The inappropriate strategy and tactics employed were field-driven and date back to 2006; the leadership of the department did not know about or authorize the use of the flawed strategy and tactics; and the department's leadership did not attempt to cover up information or mislead Congress about it."
Holder said he referred the matter to the inspector general's office last year.
"First, Kenneth Melson, the former acting director at ATF, has retired from the department, effective immediately," Holder said. " ... Second, those individuals within ATF and the U.S. Attorney's Office for the District of Arizona, whom the OIG report found to have been responsible for designing, implementing or supervising Operation Fast and Furious, have been referred to the appropriate entities for review and consideration of potential personnel actions. Consistent with the requirements of the Privacy Act, the department is prohibited from revealing any additional information about these referrals at this time.
"Finally," he added, "I have accepted the resignation of Deputy Assistant Attorney General Jason Weinstein, a longtime career prosecutor who most recently served in the Criminal Division where he led our violent and organized crime, computer crimes and intellectual property enforcement efforts."
Holder praised both departing officials.