The zoning here is pretty different than in the US though. The government created a national, unified zoning standard consisting of 12 zones.
Local governments can split their land into more-or-less arbitrary regions, and choose which zone type they want each region to have. They also have some control over how large the resulting buildings can be in each region by mandating the maximum ratio of floor space to land area for each region.
The main difference between Japanese and American zoning rules is that in the US, the zones are exclusive where-as in Japan they are (mostly) inclusive.
There's a fascinating writeup about it here: https://urbankchoze.blogspot.jp/2014/04/japanese-zoning.html