In the Japanese version, two games featured in the Nintendo Chronicle list are Jump Super Stars and Jump Ultimate Stars, a duology of Smash Bros.-styled fighting games released for the Nintendo DS that serve as crossovers between several Shonen Jump properties. Coincidentally, both games feature Goku from the Dragon Ball series, a highly-requested non-gaming character for the Smash Bros. series.

Of the various regional versions of the Chronicle sub-mode, the Japanese list is the closest to a complete list of games published by Nintendo up to December 2007.

However, various old webpages on Nintendo of Japan's website that similarly compile all Nintendo-published games for a particular console list some games that were not in the Chronicle:

• The Super Famicom page includes several games that were released exclusively through the Nintendo Power service (not to be confused with the North American magazine of the same name) and never received a standard physical release.
Additionally, all games in the Chronicle that were originally released for the Nintendo Power service would use their release dates for their standard physical release (e.g. Fire Emblem: Thracia 776 was first released via Nintendo Power on September 1, 1999, then released on cartridge on January 21, 2000; the Chronicle uses the latter release date for the game).

• The Game Boy page includes another Nintendo Power-exclusive, Balloon Fight GB, the Japanese Game Boy Color release of Balloon Kid.
Oddly, Super Mario Bros. Deluxe, despite being a Nintendo Power-exclusive title in Japan, is still listed in the Japanese Chronicle.

• The Nintendo 64 page includes games by Rare not based on pre-existing properties (both Banjo-Kazooie games for the system, Blast Corps, Jet Force Gemini, and Perfect Dark), three Star Wars titles (Star Wars: Shadows of the Empire, Star Wars: Episode I - Racer, and Star Wars: Rogue Squadron) and F-1 World Grand Prix.

• The Game Boy Advance page includes Oriental Blue: Ao no Tengai.
Additionally, while Nintendo has published every game in the Famicom Mini series (known as Classic NES Series in North America and NES Classics in Europe), only the ports of first-party titles were included in the Chronicle.
The 2005 re-release of Famicom Mini: Super Mario Bros. was also excluded from the Chronicle, likely due to that version simply being a re-release to commemorate the 20th anniversary of the original Super Mario Bros.

• The GameCube page includes Final Fantasy Crystal Chronicles and Baten Kaitos Origins.

• The Nintendo DS list includes the Nintendo DS Digital TV Tuner peripheral.

• The Virtual Boy and pre-2008 Wii webpages have completely identical game lists to their Chronicle counterparts.