- In Germany, the movie was marketed towards very young children, and many frightening or intense scenes got removed or edited. These include:
- Most shots of the Rahkshi opening their headplates to reveal their tentacled faces, with the exceptions of the brown Rahkshi roaring for a second time after Tahu surrounds it with fire, the white Rahkshi screeching as Takua and Pewku approach it in Onu-Koro, the red and black Rahkshi moving about in Onu-Koro, and the white and black Rahkshi screeching as they're defeated at the end.
- Tahu's swords landing next to Jaller.
- Makuta creating the first three Rahkshi.
- The green Rahkshi's hand rising out of the destroyed shrine.
- Much of the siege on Ta-Koro is cut, including the Rahkshi menacing its people, Gali grabbing Hahli out of harm's way, and most of Tahu's fight with the green Rahkshi. The editing is very choppy, with Tahu inexplicably lying on the ground with the green Rahkshi over him, then their positions being suddenly reversed without showing how any of this happened.
- The shot of the three Rahkshi flying toward Takua and Jaller inside the ice crevice is cut, as is the following shot of them flying over Kopaka's unconscious body. Strangely, the former shot is repeated a few seconds later.
- Makuta's eyes floating in the darkness after Takua turns down his offer.
- Pohatu and Onua engaging the three new Rahkshi only to be beaten by them is cut entirely.
- The poisoned Tahu attacking Gali. The scene cuts just as Tahu gets up.
- The Rahkshi ambushing and climbing after Takua on the "chimney" is cut, and so is Pohatu pinning the red Rahkshi to the wall. A wipe effect jumps to the scene of the two remaining Rahkshi running toward Pohatu and Onua, making it appear this is the first time they fight.
- Jaller being killed by fear power is shortened, Makuta only says "Fear me" once.
- Jaller's death scene is severely shortened. The moment when Jaller dies is cut, but the audio is heard. Takua looking at his body with sorrow is cut and his subsequent closeup is also shortened.
- The Kraata worm slithering into Makuta's lair.
- Much of Makuta's fight with Takanuva is cut.
- The Japanese dub has the characters refer to each other by name a lot more than the original dialogue, and Lewa even calls Graalok the Ash Bear by name instead of only calling her an Ash Bear.
- A version of the movie with a special extended ending aired on Cartoon Network (U.S.) and ABC Television (Australia) in 2004, before the release of Bionicle 2: Legends of Metru Nui (2004). It contained additional narration by Turaga Vakama (Christopher Gaze) during which clips from that movie played. The narration also explained that Mata Nui has not awakened yet, which is a point the original movie was somewhat vague on.
- The Hungarian dubbing did away with Lewa's characteristic way of speaking. He instead talks normally.
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