First, taking a rough average (and noting that the more populous prefectures have had smaller losses), you'd get a population loss of 5 to 10%, which is not borne out by other population statistics - the population in Japan is currently a couple of percent below its peak, which was somewhere around 2009.
Second, take a look at the figure for Akita. Assuming that some babies were born in Akita in the last ten years, then over a quarter of the population has died or moved out of the prefecture in the last 10 years. Even with a population as old as rural Japan you wouldn't expect a quarter of the population to die in 10 years, and if they have moved, where have they moved? All the other prefectures apart from Tokyo are showing population losses.