Japan actually has a lot of space that is barely inhabited or not all--most it in its mountains. The land is simply too rugged and remote to be developed into anything other than tree farms (which are bad for the environment, I might add, since one-species 'forests' typically destroy the complex watersheds that help prevent floods while creating everything from pristine trout streams to seafood-rich estuaries).
Many Japanese refer to the 'countryside' or rural Japan as 'inaka', but compared to North America, the inaka of Japan is often quite densely populated and developed. (Think New Jersey or Delaware more than anything else).
This means that universities in 'rural' Japan still have to build UP in order to create space for classrooms, research laboratories and offices. This is more of a challenge than many might think because so many parts of Japan are hazardous earthquake zones where highrise development has been severely restricted.
Take for example two of the universities in Fukui City, where I live. Both the University of Fukui (a former national university) and Fukui University of Technology (a private university) have built highrise buildings on their main campuses in order to make space.
University of Fukui's highrise building (actually two buildings connected) in the sun of a rare fine November day.
The photo below has at its center the highrise building of Fukui University of Technology, which is about 1 mile due west of the University of Fukui. Both universities' main focus is their science and engineering programs, although University of Fukui recently added a college of medicine through a government-forced merger with a former national medical college.