A tomb maybe?
It does look like one, and the sheer size of it (about two storeys high and with a diameter of perhaps two metres) would suggest a very important personality. But this is not on a graveyard, but in the middle of a standard residential neighborhood. Imperial tombs, the very old ones at least, are large and located all over the city, however, they have a distinct look that is very different from this here.
A memorial perhaps?
Could be, but there is a meadow around it with a stone fence, and it is not publicly accessible.
So, what could it be? In fact, it is both a tomb and a memorial. It belongs to Kyoto University and is meant for the people who donated their body to science.
I am not sure whether this monument really hold physical remains – that is, a few bones of each person – like a normal Japanese tomb, or maybe just a list of names, or other things that are more symbolic. But just the fact that somebody took the time and effort to build something like that, does show an enormous amount of gratitude. It makes me happy.