Her retirement was effective immediately.
The comments -- in which she said Israelis should "get the hell out of Palestine" and go elsewhere -- also led to a Bethesda, Md., high school to cancel Thomas's appearance as a commencement speaker.
"I deeply regret my comments I made last week regarding the Israelis and the Palestinians," Thomas said in a statement issued by Hearst News Service, her employer. "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."
During a press briefing Monday, White House spokesman Robert Gibbs called Thomas's remarks "offensive and reprehensible."
"I think she should, and has, apologize," Gibbs said. "Because, obviously, those remarks ... do not reflect, certainly, the opinion of, I assume, most of the people in here and certainly not of the administration."
Walt Whitman High School Principal Alan Goodwin said he discussed whether Thomas should speak at the June 14 exercise with one of Thomas's nieces after objections were raised about the reporter's appearance at the high school, The Washington Post reported Monday. The sides agreed Thomas would not speak at the event.
Thomas, 89, who covered the White House for decades, made her comments during an interview that later was posted online.
Thomas wrote for United Press International for more than a half-century and later for Hearst newspapers, covering every president from John F. Kennedy to Barack Obama.