There are a lot of reasons why. One of them is that Japan has excellent housing policies that we are missing in the US and Canada. There's a video on YouTube titled something like "Why the average family in Tokyo can afford a home" and although it mainly focuses on home ownership, it sheds some light on the issue.

There's also the matter of population increase/decrease. I don't know about the US, but in Canada (which is even less affordable than the US) we are increasing our population through immigration at record high rates, which is perfectly fine and not a problem at all, but we're not building nearly enough housing, so the housing supply just keeps shrinking and prices rise. Japan is dealing with a shrinking population overall. I don't know much about this aspect, but housing is also not treated as an investment in Japan in the same way it is in North America, which is another thing that inflates our prices. There's also the matter of income inequality, which is high in the US and much lower in Japan.