In this film, Hiroshi Koizumi reprises his role of Professor Shin'ichi Chûjô from the original Mothra (1961), which he starred in 40 years earlier. According to director Masaaki Tezuka, he had to confirm with producer Shogo Tomiyama that Koizumi would be involved in order to start writing the script.
The monster whose dead body washes up on the shore was originally intended by director Masaaki Tezuka to be Anguirus, but producer Shogo Tomiyama convinced him to change it to the less popular Kamoebas to avoid fan outrage since Anguirus was a historic ally of Godzilla. Kamoebas on the other hand is a much more obscure monster, having only appeared in Space Amoeba (1970), incidentally a film that director Masaaki Tezuka also happened to be a big fan of.
This was the first Godzilla film ever to be completed just in time for its preview showing at the Tokyo International Film Festival. All previous Godzilla films since Godzilla vs. King Ghidorah (1991) were screened there around a month before their usual general release date (early-mid December), but were still busy finishing up post-production. According to director Masaaki Tezuka, the film had the exact same budget as it's predecessor Godzilla Against Mechagodzilla (2002), though they were able to get away with more building destruction effects for this film.
Serves as a direct sequel to Godzilla Against Mechagodzilla (2002), the only film in the Millennium series to share continuity with another film in the same era. Godzilla Against Mechagodzilla (2002) was originally not going to have a sequel, with producer Shogo Tomiyama laying out 4 different story treatments for Masaaki Tezuka. Tezuka's first thought was, "I've gotta do this again?" as he was meant to just pick one, though he found the treatments Toho offered to be boring. Tezuka instead wrote a story treatment overnight and presented it to Toho which became the basis for the final film.
Before the film's official DVD release, fans had to make due with bootleg translations. One particularly egregious mistranslation stated that Kameobas' death was because it had its cervix torn out. Though Sony's subtitles are improved from the bootlegs, they nevertheless have the same "dubtitles" problem as the rest of the Godzilla films released by Sony.