[5] In 1883, the volcano on the island of Krakatoa begins to erupt, terrorizing the children at a mission school in Palembang on nearby Sumatra.

In Anjer, Java, the steamer Batavia Queen, commanded by Captain Chris Hanson, takes aboard passengers: Douglas Rigby, owner and operator of a diving bell; balloonists Giovanni and Leoncavallo Borghese; diver Harry Connerly; Connerly's mistress Charley Adams; four female Japanese pearl divers led by Toshi; and Laura Travis, who had an extramarital affair with Hanson in Batavia.

When she asked for a divorce in order to stay with Hanson, her husband left her, taking both Peter and a fortune in pearls with him aboard the steamer Arianna.

The Arianna had sunk off Krakatoa, and a guilt-ridden Laura, fearing that Peter had died, had spent a year in a mental institution.

Colonial authorities arrive just before the Batavia Queen departs and force Hanson to take 30 convicts and their jailer aboard for transportation to Madura Island.

During the voyage to Krakatoa, her crew and passengers observe strange phenomena: seabirds swarming in huge flocks by day, a series of fiery explosions erupting from the sea, and a high-pitched, ear-splitting sound like that of escaping steam.

They jettison the useless engine to reduce weight and are blown clear by a volcanic explosion which sets their balloon afire.

Hanson hails a passing junk and is informed that the school's staff and students had fled Palembang that morning, intending to sail to Java.

At sea, Hanson, Laura, Peter, Rigby, Leoncavallo Borghese, the refugees from the mission school, and the ship's crew ride out the tsunami successfully aboard the Batavia Queen.

[11] In an unusual approach to making the film, the producers of Krakatoa, East of Java had the special effects scenes shot before the script had been completed.

In 1965, Lourié scouted the coast of Spain for a suitable steamer for use in the film as the fictional Batavia Queen; ultimately he chose a cargo ship – a former passenger-cargo ship employed as a tramp steamer between Spain and Morocco – he found unloading coal at a pier in Bilbao whose captain said she had been built in England sometime around 1880.

Lourié tried to disguise the miniature Batavia Queen's lack of a crew or passengers as she gets underway for Palembang, slowly picking her way through a narrow passage under a rain of lava bombs while Krakatoa erupts nearby, by enveloping her in smoke.

[16] In addition to its challenging special effects, the makers of Krakatoa, East of Java encountered various difficulties during the film's production.

[15] While apparently conceiving Krakatoa, East of Java overall as a family-friendly adventure story, the producers also opted to attract a more adult audience by including some sordid and racy elements: the tortured relationship between Connerly and Charley and Laura's extramarital affair with Hanson, as well as a striptease Charley performs for Connerly in their state room.

[15] Kowalski said "We had more than our share of problems because you can't control such varying conditions as weather, sea, children and animals.

The catastrophic 1883 eruption of Krakatoa destroyed most of the uninhabited island and generated tsunamis exceeding 30 meters (100 feet) in height that struck the western coast of Java and southern coast of Sumatra, killing about 35,000 people, while a pyroclastic flow from the volcano that traveled across the Sunda Strait killed about another 1,000 people on Sumatra.

Hanson's statement early in the film that Krakatoa had been quiet for 200 years is accurate – the last eruption prior to 1883 appears to have been in 1680[18] – and his view that the ongoing volcanic activity on the island, which had begun in May 1883, did not pose a threat to anyone not actually on Krakatoa itself reflected the attitude of many people in the area during the summer of 1883, some of whom treated the erupting volcano as a tourist attraction.

The Batavia Queen finds the mission school in ruins and ablaze because of Krakatoa's eruption; although Krakatoa's eruption was audible in Palembang and the air pressure wave from its final explosion was strong enough to shake the walls of houses and cause cracks to appear in some, the town did not suffer the serious damage implied by the condition of the mission school in the film.

[24] The huge tsunami that engulfs Anjer and its lighthouse in the film's climactic sequence is consistent with the wave that struck the west coast of Java on the morning of 27 August 1883, rising to a height of 40 meters (130 ft) at Merak and destroying both Anjer – where it was 10 metres (33 ft) tall – and the Fourth Point Lighthouse.

[15] Vincent Canby in The New York Times was one of those disappointed with the special effects, claiming that he recognized "volcanic rock that had flown by me before.

"[29] Stanley Newman in Cue magazine called it "simple-minded fun" and Francis Herridge in the New York Post had kind words for its recreation of the devastation.

[28] The geographic error in the film's title of placing the doomed island east of Java was widely mocked in the reviews.

Krakatoa, East of Java reached number one at the US box office in December 1969 following its second run showcase release in New York.

[30][31] Based on the cities used by Variety for their weekly box office chart, it was the seventeenth highest-grossing film of the year in the United States.

[15] Although it originally had a running time of 127 minutes (not counting overture, intermission, and exit music included in the 1969 theatrical release), the movie has often been seen since then on television and in 16 mm prints in a truncated 101-minute version, with some scenes shortened or deleted.

[15] In the episode "Someone to Watch Over Me" of the series Frasier, one of the titles between sections reads "KRAKATOA, WEST OF JAVA (THE MOVIE WAS WRONG)".

In the final episode of Eerie, Indiana, one character can be heard saying on the phone, "Who cares if Krakatoa isn't really east of Java?

In 1982 the French group Indochine wrote the song, À l'est de Java, narrating the story of the movie.

An exterior shot of the Cinerama Dome in the 2019 film Once Upon a Time in Hollywood depicts the theater in 1969 advertising Krakatoa, East of Java.