The solution here is to build more higher-density housing options. Tokyo has very affordable real estate because dwellings are appropriately-sized for dense urban lifestyles and are nearly uniformly mixed-use buildings with retail space on ground floors and residence/office above. Combine this with lax zoning and you have a recipe for affordable housing.
Comparing this to my own city of Melbourne, Australia: high-density dwellings are generally constrained to innercity suburbs and are still seen as undesirable compared to free-standing homes or semi-detached houses. Councils restrict the development of new high-density or mixed-use buildings for what amounts to NIMBYism. Inadequate public transport in the growth areas of the Northern and Western suburbs increases dependence on roads and freeways.
There are options to support affordable living in cities that don't involve covering our farmland and wildlife reserves with uniform white plaster cubes.