Previously, the title was held by Pokémon Red/Green/Blue, which has sold 10.23 million copies in Japan since 1996. The Game Data Library project writes about this.
On account of Animal Crossing: New Horizons 10.45 million copies sold in the country. Together with her, the top five includes Pokémon Gold and Silver (7.17 million copies), Super Smash Bros. (6.81 million copies) and Super Smash Bros. Ultimate (6.65 million copies).
Note that Splatoon 3 has already managed to get to the 17th place in the rating, whose release took place quite recently – on September 9. Only Japanese gamers have bought it over 5 million times. As Nintendo reported yesterday, the game has sold 7.9 million copies worldwide.