Its a complex and multi-layered issue, but the short gist of it is that many houses have become effectively worthless, there are thousands of abandoned properties as they are often impossible to sell, whether they are liveable or not, and there is no incentive to hold onto property and maintain it as the value always depreciates.
In most countries, a home will appreciate in value slowly over time, with some fluctuation, but in general it is a good idea if you can afford it, there is incentive to maintain and upgrade the property as it can be sold later in life or passed down to family. The Japanese market has some of that in valuable areas of course, well built up to code homes, with nearby access to public transport and services, same with older historic homes that are worth the cost of upkeep for cultural reasons.
The overall mindset is also different, a home is a depreciating asset, that will wear out and eventually need to be demolished and rebuilt from scratch.
There are a few videos on YouTube analysing it from different perspectives (just search Japanese housing market), and there are multiple perspectives, one being that treating housing as a valuable, appreciating asset is spurning an out of control market with ever increasing pricing pushing home ownership further and further away from the average person and Japans mindset of the home as a tool rather than an asset is a positive. But on the other hand going too far in the other direction where there is zero incentive to build a home that will last generations unless you are highly wealthy to begin with, no incentive to maintain or upgrade the building, they are simply a tool, a utility, an object that you need to have but is a depreciating asset to eventually die and be replaced with the next cheapest option.
It’s a completely different mentality that has also led to its own problems, instead of the homes not being affordable because of an increasing market, they are cheap but often entirely useless without great costs to bring them up to liveable conditions or modern codes and standards, but then there is little incentive to do more than the bare minimum because you will never sell it for more than you paid, it will be worth significantly less after you have spent your years in it.]
This is made worse by the lack of young people and ultra low immigration, the cheap houses that could be considered liveable or could be financially viable to bring up to standard have no interest because they are in dying country towns or rural areas with no reason to move there, there are no young people moving back to rural areas like we see in other countries because the home is simply a place to live, not an asset worth moving out of the city for, a dying town will die in japan, whereas other countries are seeing increasing rural growth due to it being the only remaining cheap housing and people having the mindset to invest in it as an asset, making it worth moving for.