Asked during an interview with NBC about Thomas' comments urging Israel to get "out of Palestine," Obama said he believes those statements were "out of line." At the same time, he said he recognized Thomas' long service covering presidents dating back to John F. Kennedy.
He said it was a "shame" that her career has ended in controversy, but called Thomas' retirement announcement "the right decision."
The 89-year-old Thomas retired Monday as a columnist for Hearst News Service.
Thomas has apologized for comments that were captured on video by an interviewer for the website http://www.rabbilive.com. In the May 27 video, Thomas says Israelis should "get the hell out of Palestine," suggesting they go to Germany, Poland or the US.
Thomas wrote on her website that "I deeply regret my comments I made last week regarding the Israelis and the Palestinians."
She added: "They do not reflect my heart-felt belief that peace will come to the Middle East only when all parties recognize the need for mutual respect and tolerance. May that day come soon."