Marlon Brando wore a small radio receiver to aid him remembering his lines. Co-star David Thewlis claimed "He'd be in the middle of a scene and suddenly he'd be picking up police messages and Marlon would repeat, 'There's a robbery at Woolworths'."
After being fired by the studio, original director Richard Stanley was rumored to have prevailed upon the makeup crew to turn him into one of the background mutants, so that he could at least keep tabs on the making of his dream project. He supposedly did not unmask himself until the wrap party.
Val Kilmer was originally cast as the film's lead but wanted his commitment to the project reduced after being served divorce papers by his then wife Joanne Whalley. This lead to him switching roles with 'Rob Morrow', originally cast as Montgomery, the Doctor's assistant. Morrow left the film after director Richard Stanley was fired, leading to David Thewlis being cast; ironically, Thewlis was one of the people Stanley originally wanted in the film.
The ship's name was originally Ipencacuanha, in H.G. Wells's book. The filmmakers changed it to Ombak Penari. In Malay/Indonesian language, Ombak Penari translates directly as Wave Dancer (ombak means wave, penari means dancer). However, to make it grammatically accurate, the phrase should be Penari Ombak instead of the other way round.
Val Kilmer initially accepted his role so that he could work with Marlon Brando. Before filming started Kilmer informed the production that he did not want to be involved in any capacity due to the creative direction of the film, but due to the massive success of Batman Forever the studio could not afford to let him go and he was forced to participate by contractual obligation.
Val Kilmer described the shoot as "crazy". Marlon Brando was still recovering from the suicide of his daughter and the day production started the French set off an underwater atomic bomb near Tahiti where Brando owned an atoll. Then Kilmer learned that he was getting divorced when he turned on the TV. Two days later the director Richard Stanley was fired by the studio due to their concerns over the direction of the film. John Frankenheimer was then hired to replace Stanley but from the start clashed with Brando, Kilmer, and studio executives regarding the direction of the film.
According to Richard Stanley, the original shooting script was changed by Ron Hutchinson's rewrites ordered by Frankenheimer, Brando, Kilmer and the studio. Frankenheimer wanted to change the basic tone of the movie and tried to merge his version with Brando's vision of Moreau. Major portions of the script were either transformed or scrapped. However, the WGA (Writer's Guild of America) kept Stanley's co-writer credit.
This film is listed among The 100 Most Amusingly Bad Movies Ever Made in Golden Raspberry Award founder John Wilson's book THE OFFICIAL RAZZIE® MOVIE GUIDE.
When Val Kilmer apes David Thewlis' staid manner of saying "the islanders", he sounds more like Marlon Brando (who he later imitates more blatantly) than Thewlis.
Towards the start of the film, a framed certificate in Swedish bears the names of Dr. Moreau, Alfred Nobel, Karolinska Institute. The Karolinska institute awards the Nobel Prize in Physiology or Medicine. Immediately after the certificate is shown, the protagonist is seen examining a display box containing a Nobel Prize.
Assassimon, the baseball bat-wielding ape-creature, seems to be a remnant of an earlier draft of the screenplay where some of the Beast People were putting together a baseball team.
Val Kilmer frustrated director John Frankenheimer so much, that, after shooting Kilmer's last scene in the movie, Frankenheimer is alleged to have said: "Cut. Now get that bastard off my set."