A Toho Video documentary released in the 1980s contained several unused and deleted takes from this film. The majority of this footage consists of alternate takes of finished scenes, such as the raids on Moscow and Paris by Rodan and Gorosaurus (respectively). Toho also filmed much more footage of the UN's defense of Tokyo, including a number of shots of missile launchers being deployed from the roofs of skyscrapers. The most notable unused shot in this feature has Godzilla thrashing the monster Manda against several Tokyo buildings. According to Haruo Nakajima, this was an impromptu act at the end of a take. This was likely removed from the finished film as both monsters were under Kilaak control and shouldn't have been fighting.
A complete English language version of "Destroy All Monsters" was supervised by Toho for international distribution. The English dialogue was dubbed by William Ross' Frontier Enterprises in Tokyo. Additionally, Toho created English titles and credits to be spliced in in place of their Japanese equivalents. This version, known by Godzilla fans as the international or export version, remained unseen in the United States until the film's premiere on the Sci-Fi Channel on January 20th, 1996. A video and DVD release by ADV followed, and Toho's English version has now supplanted the original U.S. release version.
In the original version it is stated that the base where the Moonlight SY-3 departs from at the beginning of the movie is located on Iwo Jima. However, in either of the English dubs it is never mentioned where the base is located.
The English version released by American International Pictures in 1969 is entirely different than Toho's export version. AIP contracted with New York's Titan Productions (previously known as Titra Sound Studios) to loop the English dialogue. Among the dubbing personnel for this version were Hal Linden and Bret Morrison. This dialogue track was included by Media Blasters in its 2011 DVD and Blu-Ray release of "Destroy All Monsters," however, newer printings feature only Toho's Japanese and English soundtracks. AIP was also responsible for several small edits to the film. In the Japanese and international versions, a sign establishing the UN Defense Center can be seen in the rubble of Tokyo. Instead of translating this sign, AIP's editors removed it altogether. Additionally, AIP deleted two shots of Minilla's antics during the climactic monster showdown. AIP also relocated the credits to the end of the picture.