The French woman told L'Equipe newspaper on Saturday that she had made a "mature" decision to call an end to her career.
"I have taken a big decision to stop swimming," said Muffat who won the 400 metres freestyle gold at the 2012 London Olympics as well as the silver medal in the 200 metres freestyle.
Muffat said she had had a disagreement with her coach Fabrice Pellerin and that that had led her to end her career,
"It will stay between us like many other things, good or bad, But I mention that because that was what started things off," she said.
Muffat, however, did not rule out completely a return to swimming. citing the cases of Michael Phelps, Laure Manaudou and Ian Phelps, all Olympic champions who retired but later made comebacks.