- The US version takes out about 9 minutes of the film and changes a lot of the dialogue.
- In the American theatrical versions, a green "The End" with a red question mark in the middle is super-imposed over the closing shot of Godzilla blowing up Shinjuku with his Radioactive Heat Beam right before the closing credits. Michael Schlesinger, the producer of the US version, did the scene in tribute to sci-fi films from the good old days, but since he was on vacation, Tri-Star used the "goofy" font, as opposed to the black blocky letters Schlesinger wanted. Either way, Toho Company Ltd. didn't like it, so Toho and Schlesinger agreed to remove the title card from all subsequent versions (on VHS/DVD and TV prints).
- Scenes deleted from the US version include:
- Some quick shots of a train station in Nemuro during the film's opening.
- After Yuki asks for directions to GPN's office, she goes into a factory-like complex, and spots a sign (with crude version of the GPN logo), with an arrow pointing up a flight of stairs. She enters the office, but since Shinoda was too busy to help her, he points to his daughter Io, who prepares to give Yuki her membership form in the next scene.
- The scene where the UFO rears right-side up (due to its recharging from the rising sun) was trimmed.
- The sequence with Godzilla's raid in Tokaimura was also trimmed. (The scene where Godzilla sets off the Blast Bombs in the lake was noticably cut, as the tremendous watery explosion was suddenly gone in the next shot, which made for a glaring continuity problem).
- In the Japanese version, said sequence ended when Godzilla was beginning to charge his Radioactive Heat Beam, but was heavily bombarded with jets, and Godzilla's aim was abruptly cut short. This was removed in the US version.
- Right after Io talks to her dad on the phone about handing the GPN's MO discs to CCI, she takes out her magnetic "pinbox" (referred to as her "summer homework" in the Japanese version), and slides a drawing of a flower into it (This was the same pinbox Shinoda used to demonstrate the effects of Organizer G-1 on the formless alien life form in the UFO, just before Godzilla rose from Tokyo Bay). This brief scene was cut in the US version.
- During the sequence where the UFO enters Shinjuku, the scene with the astonished taxi driver in a confusion of heavy traffic was longer in the Japanese version (This scene was a parody of a similar scene in Independence Day (1996)).
- When Shinoda finishes decoding the information on the Millennian aliens on Yuki's laptop in the soon-to-be-detonated building, he is about to run out with it until he sees the English word "Millennium" on all of the monitors in the room. He reads "Millennium" in English. This scene was completely removed in the US version.
- In the Japanese version, just after the Blast Bombs are detonated in the top section of the Shinjuki media building (with the UFO perched on top), and the UFO was completely unscratched, it transmits a bilingual (Japanese/English) "message" on all media throughout the city, with words (and images of space exploration and military machinery) like "Earth," "Destruction," "Alteration," "Conquest," "Erase," "Suppression," "Dominate," "Terror," "Eternity," "Prosperity," "Revolution" and finally, "Kingdom." This was just before the UFO destroys the rest of the building (with Shinoda inside trying to escape).
- The scene where Shinoda tries to escape the collapsing building through an elevator was fixed in the US version. In the Japanese version, one is led to believe that Shinoda "perished" in the falling rubble (we hear his scream in that same scene).
- Toho produced an English version that retained the original sound and music. However, TriStar opted to re-record the dialogue and also changed much of the sound, including modifying Orga's roar and supplementing Godzilla's roars with those from Godzilla (1998). Additional music was composed by J. Peter Robinson to replace some of the original score.
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