The president also brushed off the suggestion of a special counsel, saying investigations by the U.S. Justice Department, the IRS Inspector General's Office and Congress should do the job.
The IG report in April said IRS employees in branch offices appeared to single out Tea Party and other conservative groups for investigation when they applied for non-political status under the Tax Code.
"I can assure you that I certainly did not know anything before the IG report was leaked to the press," Obama said.
"My main concern is fixing the problem, and we began that process yesterday by accepting" the resignation of the acting IRS chief.
"It is just unacceptable that there should be a hint of" politics in how the IRS conducts business, Obama said
Obama said the administration was going to "work with Congress to make sure we know what happened."
The president cited the multiple investigations and said "between those investigations we're going to find out what went wrong. ... I think we're going to be able to fix it."
Obama appeared at a joint White House news conference with Turkish Prime Minister Recep Tayyip Erdogan.