Klaus Kinski was a major source of tension on set, because he fought violently with the crew and raged over trivial matters. The natives were very upset about his behavior. Werner Herzog has claimed that one of the chieftains offered, in all seriousness, to murder Kinski. However, Walter Saxer, the production manager of this film, later confirmed that Herzog's story was not true.
After a Peruvian logger was bitten by a deadly snake, he immediately cut off his own foot with a chainsaw to prevent the spread of the venom. Werner Herzog commented, "It was a good decision, he lived."
The film was shot during one of the region's driest summers on record. Indigenous Amahuaca launched a hit-and-run raid on the film camp. One man survived an arrow through his throat. His wife was hit in the stomach, necessitating eight hours of emergency surgery on a kitchen table. According to Werner Herzog, "I assisted by illuminating her abdominal cavity with a torchlight, and with my other hand sprayed with repellent the clouds of mosquitoes that swarmed around the blood." Herzog decided against a revenge attack, believing it would be bad for relations.
A real 365-ton steamship was moved over a mountain, with a bulldozer. Throughout Klaus Kinski's displeasure of making the film, he was truly astonished by the feat and his reaction was included in the film.
Cinematographer Thomas Mauch's hand was split open trying to film the climax. He underwent a 2½ hour operation to put his hand back together again, without anesthesia. As he screamed and thrashed in agony, one of the camp prostitutes calmed him by pressing his head between her breasts.