The Japanese version of the game was released later than the Western release, allowing for Treasure to tweak some aspects of the game, the most notable being that Black Jewel has a second boss phase with completely new music. Black Jewel floats down to the arena where Wario must attack it until it gets dizzy so he can perform a Mad Move on it. Black Jewel also has new animations after each big hit it receives, retracting its arms and spinning as it glows.

Pausing and waiting 50 minutes will cause Wario to stop making the noises he usually makes and say "sorry" to the player.