Do you have a source for that? According to this article[1] which is summarizing an official Japanese zoning document [2] they have 12 well-defined zones.

They're overall more relaxed about mixed-use zoning, but they do have exclusively industrial zones, and exclusively residential (with small shops & schools) zones.

1. http://urbankchoze.blogspot.nl/2014/04/japanese-zoning.html

2. http://www.mlit.go.jp/common/000234477.pdf