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The furor over the program prompted the head of the ATF to resign after a Border Patrol agent was shot with weapons that were linked to the Fast and Furious operation.
President Obama said during a press conference Thursday that he had "complete confidence" in Holder.
"He's indicated that he was not aware of what was happening in Fast and Furious. Certainly I was not. And I think both he and I would have been very unhappy if somebody had suggested that guns were allowed to pass through that could have been prevented by the United States of America," Obama told reporters.
"He's assigned an inspector general to look into how exactly this happened," he added.