Gates made the comment bout his book "Duty: Memoirs of a Secretary of War" during an interview on NBC's "Today" show.
"The book has sort of been hijacked by people along the political spectrum to serve their own purposes, taking quotes out of context," he said. "It's sort of the political warfare in Washington that I decry in the book."
He also defended the book as even-handed.
"I don't vilify anybody and I make clear that I have a lot of respect for both President [George W.] Bush and President Obama," Gates said.
Gates, who served in both presidents' administrations, has been criticized for statements in the book that Obama had reservations about the war in Iraq.
He said during the interview he "absolutely believed" Obama supported the surge of U.S. troops in Iraq, although in private conversations "he would express these reservations about whether it was working. But the decisions were right, and I believe that he believed it would work."
Gates said he never claimed in the book that Obama opposed the surge only for political reasons.
"What I say in the book was that the president conceded that a lot of opposition to the surge had been political," said Gates. "He never said that his opposition was political. In fact, his opposition was consistent with his opposition to the war all along."