Obama faced criticism for praising Harris.
The New York Times wrote that President Obama late on Thursday night called Harris and apologised to her for telling a group of wealthy donors that she is the "best-looking attorney general in the country.
"He did not want in any way to diminish the attorney general's professional accomplishments and her capabilities," White House press secretary Jay Carney said at a White House briefing.
Carney said Obama apologized for creating the distraction.
"He fully recognizes the challenges women continue to face in the workplace, and that they should not be judged based on appearance," Carney said.
At the last stop of a fundraising swing in California on April 4, Obama singled praised Harris.
"She is brilliant and she is dedicated and she is tough, and she is exactly what you'd want in anybody who is administering the law, and making sure that everybody is getting a fair shake," he said at an Atherton, California.
"She also happens to be by far the best-looking attorney general in the country - Kamala Harris is here," Obama added amid applause, according to a transcript provided by the White House.
"It's true. Come on. (Laughter.) And she is a great friend and has just been a great supporter for many, many years," he said of the first woman attorney general of California.
Harris, daughter of an Indian mother and an African-American father, was the first elected official in California to endorse Obama during his 2008 run for the White House and campaigned for him during his 2004 Senate run.
But Obama's playful remarks set of a little storm. "Obama calls Kamala Harris 'best-looking:' Accurate, but sexist?" wondered the Los Angeles Times.
"Does merely stating the obvious make the president sexist? More wolfish than sexist, I'd say. And this may be a little problem he needs to work on," said columnist Robin Abcarian.