This film was originally written to star King Kong, as Rankin/Bass Productions had provided Toho with the license to the character in order to produce a tie-in film for Toei's animated TV series King Kong (1966), which they co-produced. However, Rankin/Bass rejected the original treatment, as they wanted director Ishirô Honda to helm the film. Toho insisted on Jun Fukuda and after Rankin/Bass backed out, Toho decided to replace King Kong with Godzilla. Toho and Rankin/Bass would then go on to co-produce El regreso de King Kong (1967), a film that was more in line with what Rankin/Bass wanted.
Director Jun Fukuda harbored a disdain for this and other Godzilla films in the series that he directed, noting he would give them all "a minus score." Fukuda was not fond of the choices forced upon him by Toho and described his experience working on the film as "pouring two cups of water into one." When Toho sent him a copy of the film on VHS, he felt it was like "opening up an old wound." Special effects director Teruyoshi Nakano noted that while Fukuda did not enjoy making these films, he was nonetheless a skilled craftsman, a sentiment shared by film historian Stuart Galbraith IV. Galbraith mentioned that when he first interviewed Fukuda, they almost got into an argument with Fukuda telling Galbraith how terrible he thought his films were while Galbraith tried to convince him otherwise. In his later years, Fukuda seemed to slightly soften his harsh opinions, as he received numerous fan letters and was surprised by Godzilla's enduring popularity.
The Giant Condor was created by taking a Rodan prop and re-purposing it for the film.
After destroying the Giant Condor, Godzilla looks down at Daiyo and touches his nose with one of his fingers (this finger corresponding to a human's index finger). This is an homage to Yûzô Kayama's popular character "Yuichi Tanuma" (from Toho's popular Wakadaishô/Young Guy film series that started with the film Daigaku no wakadaishô (1961)), who did the same thing.
The Mothra imago in this film is the remaining larva from Godzilla contra Mothra (1964). She metamorphosed from one of the two Mothra larvae from that film. The same larva returned in the next film in the series.