It's not Japanese, but it is an animated feature, and a serious one at that - The Plague Dogs. I watched that last night, and it broke my heart to a million pieces, and each of those pieces broke to pieces, and each of those pieces broke...which just sort of became dust at that point, sooo I just have this heart dust floating around my chest.
It's a very sad movie, very realistic, about two dogs who escape from a lab of terrible experiments and cruel tests. It just keeps going downhill to a bittersweet conclusion, at which point I was sniffling and sobbing like a baby.