This is one hypothesis put forward by News Scientist, which is reporting (subscription only) possible reasons why Grey Whales of Siberia are stinking. Read more about the phenomenon in National Geographic News, posted last summer.
Lee Cooper at the University of Maryland Centre for Environmental Science in Cambridge, reckons food shortage may have caused the whales to switch their diets, altering their metabolism and producing ketones. They may enter the state known as "ketosis" in which they burn fat for energy, which in people causes bad breath.
Scientists in Mexico are trying to collect samples of their breath (how?!) for gas chromatography, which is how they worked out why people on the Atkins diet stank.