In Japan, zoning is the responsibility of boards appointed by the national government in charge of zoning large regions, rather than being a responsibility of local governments, but it is not truly done at the national level.
When the decisions are made by local governments, they are dominated by property owners who own real estate that is already in place who want to maximize their property values. The interests of people who do not currently own property in a municipality who want to, for example, develop more affordable housing options in a way that reduces the property values of existing property owners near where the affordable housing would be built in that municipality, basically aren't considered. But, if you do zoning at a larger scale that doesn't just have political pressure on zoning officials that is dominated by local existing property owners in a municipality, you tend to get less restrictive zoning rules.
You see something similar in California where state officials have recently forced local governments to relax their zoning restrictions due to essentially the same analysis of political influences on zoning officials.
This is an important reason that Japanese real estate economics are quite different from most developed countries. Tokyo, for example, has seen far less of a surge in housing prices (and more generally real estate prices) than other major international cities.