The whistleblower alleges that the agency intentionally let more than 1,700 guns be illegally trafficked to Mexico.
"I did not authorize it; Eric Holder, the attorney general, did not authorize it. He's been very clear that our policy is to catch gun-runners and put them into jail," Obama said.
Clarity about what exactly took place during Project Gunrunner may come soon: Holder has asked the Justice Department's inspector general to investigate.
Rep. Darrell Issa (R-CA), chairman of the House Oversight and Government Reform Committee, has also launched his own probe. He told a radio show that he has four investigators working full-time to try and understand why guns were allowed to "walk" over the border without any safeguards in place.
Obama said that he would hold someone responsible if, indeed, a mistake was made.
"We have to make sure that we're enforcing the kinds of measures that will stop the flow of guns and cash down south that is helping to fuel these transnational drug cartels," he said.
"There may be a situation here in which a serious mistake was made," he said. "If that's the case, then we'll find out and we''ll hold someone accountable."
Current relations between Mexico and the U.S. are strained: The U.S. ambassador to Mexico Carlos Pascual resigned Saturday after diplomatic cables were released by WikiLeaks showing Pascual criticizing Mexican authorities.
Watch the interview with Obama below: