Human: Fall Flat has sold 2 million copies in Japan, as revealed by Teyon Japan yesterday.
This makes Human: Fall Flat one of the best-selling Western games in Japan.
Also note that the Switch version seems to have sold a bulk of these copies, seeing as only 600k copies had been sold prior to the Switch version's release.
It is likely that other contemporary indie games have sold a million or more copies in Japan, including Undertale, Inside, and Stardew Valley, all of which have charted well on the Switch eShop.