It's true that Japan has a lot more ethnic homogenity than most countries, but this is is a misleading statistic. The Japanese census considers all people with Japanese citizenship to be simply "Japanese" regardless of their race.

There have been 559,789 naturalizations total from 1952 to 2018: http://www.moj.go.jp/content/001180510.pdf

Many of those have probably died by now, but likely not without leaving a few descendants. So there may be a million or so Japanese citizens with a family background involving migration within the last few generations.

Ainu, Ryukyuans and Burakumin should probably also be counted as "non-homogeneous", even though they're not "foreign".

besides from naturalizations, there's also quite few half-japanese people that acquire citizenship by birth-right. Although I'm pretty sure the wide consensus in Japan is that half-japanese is considered non-japanese, so the number would go down a little bit more.

Do you have a source for that? It's certainly not the legal case.