Speaking to the editorial board of the Argus Leader in Sioux Falls, S.D., the Democratic New York senator said, "We all remember Bobby Kennedy was assassinated in June in California."
Some political observers criticized Clinton's reference to Kennedy's slaying, many seeing in it a suggestion that Obama, who is black, is at risk of assassination.
"Her remarks were not about Sen. Obama. They had nothing to do with him," Clinton senior adviser Howard Wolfson said Sunday on CBS' "Face the Nation."
Wolfson said Clinton has since clarified her comments.
"She very quickly made clear what she meant if she caused anyone any discomfort or pain because it is obviously a very sensitive topic," Wolfson said. "She apologized. But she was talking about it in an historical context."
Obama, the junior senator from Illinois, has said he accepts Clinton's explanation.