Once filming began, Peter Brook largely dispensed with the script and encouraged his young cast to improvise. He shot over 60 hours of footage which was then edited down into a 90-minute film. Consequently, there is no screenplay credit.
During post-production in Paris, the director Peter Brook and editor Gerald Feil couldn't get the right effect for the sound of the dead pilot's parachute blowing in the wind. The book called for a 'plopping noise', and nothing seemed to sound right. Eventually Gerry found the perfect sound by slowing down a recording of his cat purring.
According to the filmmaker's commentary on the DVD version of this film (at 0:06:09), because of the loud noise from the sea and jungle on the beaches of the islands on which the movie was set, none of the dialogue could be recorded synchronously at the actual locations where the scenes were filmed. Instead, at the end of each day, the actors would be taken to a quiet location in the interior of the islands, where the dialogue for the scenes they had just filmed would be recorded from memory to be re-mixed, word by word, during the editing process. The one exception is the scene where Piggy tells some of the younger children how his hometown of Camberly got its name (which is also the only scene in the movie which is not based on a scene in the original book.)
The 60 hours of film from the 1961 shoot was edited down to 4 hours, according to editor Gerald Feil. This was further edited down to a 100-minute feature that was shown at the 1963 Cannes Film Festival (May 9 to 22), but the cuts necessitated that new audio transitions and some dialog changes be dubbed into the film more than a year after shooting. The voice of James Aubrey, who played Ralph, had dropped three octaves and was electronically manipulated to better approximate his earlier voice, but it is still significantly different. Tom Chapin, who played Jack, had lost his English accent and another boy's voice was used to dub his parts. The U.S. distributor insisted the film be further edited to 90 minutes, so one fire scene and scenes developing the character Ralph were cut.
During the first week of film shooting on the Island of Vieques, Puerto Rico, the Bay of Pigs Invasion began. This impacted filming because the wounded were evacuated to the U.S. naval hospital on Vieques.
In 1996, 35 years after the film was made, the BBC created a documentary about the making of the film called "Time Flies", which reunited the main cast and crew on the beaches of the Caribbean where it was filmed; an article written by one of the actors, Tom Gaman, mentioned that of the boys, only the one who played Ralph (James Aubrey), pursued an acting career. Others went on to have very different ones: Gaman became a freelance forester in Inverness, California; Hugh Edwards (Piggy) became an engineer for a Russian firm; Tom Chapin became a gold mine geologist in Nevada and the twins David Surtees and Simon Surtees (Samaneric) remained together, living with their families in the UK and working as a guidance counselor and political administrator respectively. (NOTE: Contrary to Mr. Gaman's article, another of the boys besides James Aubrey, Nicholas Hammond, who played Robert, had a quite extensive film AND TV career, playing, among other roles, one of the children in The Sound of Music (1965) and the title role in TV's The Amazing Spider-Man (1977).)
The name of the boy who is whipped at the end is Piers in the movie (though his name is not mentioned in the dialogue), but was Wilfred in the book. The reasons that Jack imposed this punishment remain unspecified in both the movie and the book.
The title of the film is left unexplained. The novel makes it clear that the pig's head on a stick is the nominal Lord of the Flies. This is a translation of the word Beelzebub. A scene that was cut short for the film was the dialogue between the infested pig head and Simon. The head would deride Simon for their efforts to find and appease the Beast. Then it would imply that the Beast is simply the boys themselves and that it is futile to escape. Although the film shows Simon in an entranced state while looking at the pig head, their dialogue was omitted from the final cut. All this back-story however clarifies the symbolic background. The boys have the inherent evil in themselves and as days passed, their animal instincts would take over (which is precisely what happens after the confrontation between Simon and the Lord of the Flies).
Although the religion of the choir is never specified in the book , the film implies that the boys belong to a Catholic or even a Protestant dogma (judging from their outfits and their British nationality). Surprisingly the boys are heard twice during the film to be chanting "Kyrie eleison" with a quite fluent pronunciation. This is a common hymn in Orthodox Church ceremonies. It stands for "Bless us Lord" in Ancient Greek.