The film was originally 94 minutes. When the film was released in the US in 1992, some intense sequences and additional material was cut to obtain a G rating and to make the film shorter. The Japanese DVD box-set and 2004 US DVD restored these sequences.
The following scenes, cut from the 1992 version, were reinstated on both the Japanese and U.S. DVD releases (Total running time of missing footage:): -Originally, the film opened with a long opening credit sequence (including the TMS logo), lasting 2 minutes and 45 seconds, set to the title theme song sung by Melissa Manchester. In addition, the end credits were originally 2 minutes and 3 seconds long (combined with what was originally the opening credits, the end credits in the 1992 version ran for 4 minutes and 30 seconds. The end credits in this version also had a 1992 copyright date, whereas they originally had a 1989 one). -10 seconds of the scene where Nemo falls from the cloud ruins. -10 seconds of the scene where Nemo tries to evade the train. -A 10 second shot of the film's logo, after Nemo wakes up from his first dream. -An entire 1 minute and 43 second scene where Nemo sleepwalks into the kitchen to sneak a pie out of the icebox, only to be schooled by his mother, because he broke his promise, about sneaking them out of the kitchen. He then hurries back to his room. This would explain why the "Remember Your Promise!" note appears again later in the film. -A 12 second scene where Nemo and Professor Genius arrive at the floor where Princess Camille is. -An entire 1 minute and 59 second scene where Nemo and Flip make mischief in the Slumberland Police Station, and then escape on Flip's flying Bird named Flap. -1 minute and 53 seconds worth of footage from the dance scene. -A 17 second scene of Nemo, Icarus, Flip, Princess and Professor walking through a spooky forest on the way to Nightmare Land. -An entire 1 minute and 16 second scene where Icarus tells the Oomps that if Nemo says the incantation to use the Royal Scepter, he will die. Nemo then reassures him that he will be just fine. -A 14 second scene where Nemo gets annoyed by the constant chanting from the Oomps and Icarus, as he tries to study the incantation. -A 49 second scene, where as Nemo and the others venture into Nightmare Land, Oompo gets burned, they lose direction, and they find themselves in a sea of black slime. -An entire 1 minute scene, where one of the Nightmare King's henchmen tells him that Nemo and the scepter have been terminated. But when the Alien Bird informs him that Nemo is still alive, he blows everyone away with his powers. -A 40 second scene where, after the Nightmare King has been defeated, Icarus looks for Nemo, only to find that he died from using all of his strength to activate the Royal Scepter. -A 6 second scene near the end, where, after waking up from his dream, Nemo apologizes to his mother for breaking his promise by taking the pie from the kitchen.