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Historical accuracy
While much of the story is historically accurate, screenwriter Petter Skavlan and director Joachim Rønning both felt the need to make the story more exciting for their two-hour feature film.

Some of the alterations from Heyerdahl's book are minor: the ship's parrot is eaten by a shark in the film; its real-life counterpart was simply washed overboard by a large wave. The film shows the crew only getting access to valuable US military equipment once they have arrived in Peru and are building the raft; whereas Heyerdahl arranged for the equipment at a visit to the Pentagon before traveling to Peru.

The film has the crew worrying about getting sucked into "the Galapagos maelstrom," with a book shown that purportedly illustrates the maelstrom. The illustration is actually artist Harry Clarke's 1919 illustration for Edgar Allen Poe's short story, "A Descent Into the Maelström," a fictional account of a whirlpool in Norwegian waters. The description of its roar, which can be heard from nine miles away, is taken directly from Poe's story. Although Heyerdahl did refer to "treacherous eddies" near the Galapagos, his chief worry there was that "strong ocean currents" could sweep the raft back towards Central America. Most controversial has been the portrait of the raft's second-in-command, Herman Watzinger. Colleagues and relatives say Watzinger in the film is unlike the real-life Watzinger, physically or in his actions. Baasmo Christiansen, the pudgy actor who portrayed Watzinger, acknowledged the physical differences with a smile. "Watzinger was tall, dark, and Norwegian Youth Champion in the 100 meter. He was everything I'm not."

In the film, Watzinger disobeys Heyerdahl's direct order and throws a harpoon at a whale shark under the boat. It was actually Erik Hesselberg who harpooned the whale shark, with the crew cheering him on. The film's Watzinger, worried about the hemp ropes' ability to hold the balsa logs together for the entire voyage, tearfully begs Heyerdahl at sea to add steel cables Watzinger smuggled aboard. Heyerdahl's book contains no such scene. When the scene was described to Watzinger's daughter, she said it never happened. "My father was a stout and confident man, and he never thought that way about the balsa logs and the ropes." Thor Heyerdahl, Jr., who worked with Watzinger, concurred in the criticism of the film's portrayal of Watzinger.

Film critic Andrew Barker commented, "It’s frustratingly ironic that Kon-Tiki’s most outrageously fantastical sequences are completely verifiable, and its most predictable, workaday conflicts are completely made up."

The movie focuses on Heyerdahl's theory that Polynesia was first populated with humans from Peru, but it ignores the Norwegian's more ethnocentric speculations that the original Kon-Tiki voyage was undertaken by a race of tall white people with red hair and bearded men. Heyerdahl conjectured that Amer-Indian civilizations like the Aztecs and the Incas only arose with the help of advanced technical knowledge brought by early European voyagers, and that these white people were eventually driven out of Peru and fled westward on rafts.