Note: None of the changes done for the PAL version were carried over.
(Credit goes to Micster for the following pictures.)
As could be expected, the logo was changed to Katakana as part of the localization process for Japan. The rest of the text in the game is usually written in Hiragana.
The password system was removed, leaving you only with the option of saving. This version remembers the Crash Bandicoot slot in your Memory Card after you first save your game, so you don't need to re-select it every time you want to save.
There is an all-Japanese voice cast for the game, and Crash speaks instead of simply using interjections. The text has all been translated into hiragana. These two changes remain consistent throughout the series.
(Video by Keiji Dragon)
Some of the character leitmotifs were changed to completely different tunes. These are Tawna, Koala Kong, Pinstripe Potoroo, Nitrus Brio and Cortex (the latter's original theme is still heard in his bonus levels, though).
To rotate the islands, you need to press L1 and R1, as opposed to Square and Circle.
Ore wa Aku Aku
The witch doctor gives you preset text hints when you collect certain masks.
A Mask For the Trip
You automatically start with an Aku Aku mask in the first level, which also gives you a text hint. As a result, the first Aku Aku box you'd usually find is no longer present.
TNT crates have a bomb symbol instead of the word "TNT" on the sides. This is something that stuck with every other game in the series.
Tawna disappears from her bonus levels once Crash reaches her. Maybe they tried to explain why Crash doesn't just grab her there by turning her into a hologram.
Even if you lose a life in a level, you are still presented with the box count screen. Additionally, Crash is only hit by a single crate, regardless of how many of them you've missed. The number of boxes you've missed is shown in the bottom text line.
The fat man is harder to beat in this version. Not only does he have 5 hit points instead of 3, but he also starts swinging his club faster and faster after the third hit.
Sunset Vista and Slippery Climb were switched with each other. This was likely done due to Sunset Vista's tremendous difficulty spike, so here it ends up appearing much later in the game. The key to Whole Hog is still found in Sunset Vista, despite its new location, making it more confusing for newcomers to figure out what exactly it unlocks.
Some colored gems have been switched around for better flow.