"On behalf of the American people, I extend my deepest condolences to the medical professionals and other civilians killed and injured in the tragic incident at a Doctors Without Borders hospital in Kunduz," he said in a statement released by the White House.
"The Department of Defense has launched a full investigation, and we will await the results of that inquiry before making a definitive judgment as to the circumstances of this tragedy," Obama said.
MSF said the aerial raid hit the main hospital building housing the intensive care unit and emergency rooms, while the surrounding buildings were left untouched.
"I have asked the Department of Defense to keep me apprised of the investigation and expect a full accounting of the facts and circumstances," Obama said.
"Michelle and I offer our thoughts and prayers to all of the civilians affected by this incident, their families, and loved ones."