Here is how it works : Japanese real estate essentials.
What kind of laws are protecting rights of your real estate in Japan ?
The civil law describes the general rules for the purchase and sales (and lease) of the property.
The civil law regulates ownership and superficies and also provide the definition of rights such as pledge and mortgage.
As a conventional individual, I think you only need to know how the mortgage works in Japan.
The land lease and building lease law, which is special law of civil law, provides
the general rules of land lease and building lease.
The act on sectional ownership of buildings provides the general rules on sectional ownership, meaning
the law is for the condominiums.
The real estate registration law is for the real estate registration system.