Ciro Guerra wanted to make a film in Colombia's Amazon region from the moment he discovered cinema. "It's a huge portion of the territory of Colombia – about the size of France – but it's a region we know very little about," he says. He had made two films that were close to home, about feelings and family. "I wanted to get away from that and take a journey to the unknown. And for a Colombian there is nothing more unknown than the Amazon. We know more about outer space." He had no idea what story he wanted to tell, only that he wanted it be something nobody had seen on screen before.

 Embrace of the Serpent is the result. It is extraordinary. Shot in a remote area with a cast of Amazonians speaking nine distinct languages, it takes elements of the real – the journals of two scientific explorers and the living traditions of the Amazon communities – and weaves them into the story of Karamakate ("he who tries"), an imaginary shaman from a vanishing tribe who travels with each of them.

The older Karamakate is played by Antonio Bolivar Salvador, who is one of only 16 surviving Ocaina people. He had performed once before in a short film for the Colombian ministry of culture but Nilbio Torres, who plays the younger Karamakate, had never so much as seen a television image. When he saw the finished film, he told Guerra he had been so frightened he almost fainted. His performance is, however, assured and forceful.

Storytelling is such a fundamental part of the culture, says Guerra, that acting seemed to come naturally to the Amazonian cast. "I was worried at first, because I thought it would be extremely difficult to explain to them what filmmaking was about. But they have this oral tradition that means they really know how to listen. They can listen for real. And that is the most important thing an actor can have."

Karamakate's first charge is German scientist Theodor Koch-Grunberg, who in real life was the first scientific writer to describe the Amazonians as "the people of the Amazon". It is 1909; "Theo" is dying of a tropical illness and, according to his local companion, only Karamakate's knowledge of rare plants can save him. (In fact, Koch-Grunberg died in 1924).

The second is Richard Evans-Schultes, considered the father of modern ethnobotany, who really did go to Colombia in 1943. Evans-Schultes' writings about the Amazonians' relationship with nature and the universe became key texts for the nascent counterculture, but Guerra's story gives "Evan", who is travelling on the United States government's dollar, more conflicted motives.

Guerra first considered making a historically accurate account of these two men's journeys. Then he realised that it was only by fictionalising the story that he could tell it from the indigenous character's point of view. "These stories are always told from the point of view of the explorers," he says. "We wanted to change that because I realised that was what was going to make the film special, providing an insight into a different way of understanding the world."

Reaching some level of a different understanding was his challenge as a writer. He worked on the script for three and a half years. "It's very difficult to learn to see things from a different point of view," he says. "We tend to think we are open-minded and accepting of difference, but the experience of the Amazon makes you realise how closed you are and how much of what you take for granted is merely a matter of perception."

He also realised he couldn't expect to apply the usual logistics of filmmaking to working in the rainforest.  Although he doesn't mention it, the legendary horror that was the making of Werner Herzog's Fitzcarraldo – during which one crew member had to amputate his own foot after being bitten by a snake and relations with the Amazonian extras were so bad that a disgruntled vanguard burnt down the set – stands as a salutary lesson to any Western director who thinks he can take on the jungle and win.

Not that Guerra tried to do that. "We wanted to make the film within the conditions of the place and we had the guidance of the communities there. Before the shoot we had a shaman work with us, to ask to the jungle for its permission. We had the protection of the place. And although we were prepared for things to go wrong, nothing really bad happened. We didn't have any accidents; we didn't have any diseases. We saw all kinds of animals but no one was eaten or attacked. So we felt the jungle was allowing us to make the film: opening up, giving us gifts."

He was adamant, however, about aesthetic choices that must have given his financiers pause. For a start, he wanted the film to be in the same black and white as the luminous photographs taken by the early Western explorers. "What you see in these image is an Amazon completely devoid of all this exuberance and exoticism," he told Cineaste magazine. "It feels like a different time speaking to you through these images." No film does any kind of justice to the vibrant colours of the jungle anyway; it was better that the audience imagine them.

He was also determined to shoot on 35mm film. Digital cameras may be light, portable and show immediate results, but only film shows every bit of information in the frame, every gradation of light, "because it captures an image; it's organic". So every three days, reels of film were sent off in a small plane to a laboratory in Argentina – the only film processor still working in South America. They would see the rushes weeks or even months later.

Of course, it was hard. A crew of 40 lived in an abandoned mining camp. There were mosquitoes and unavoidable practical problems. Shooting on the Amazon River itself, in particular, was close to impossible because while they might be shooting only one boat, there were four more boats with camera, sound and so forth that had to be kept in alignment on a roiling river with the one in shot. "But however hard it was shooting in the jungle, I think I found it harder to come back to the modern world,"  Guerra says.

"Because once you start looking at the world from another point of view, nothing is the same. If I had to sum it up, I think I learned to be lighter. I shed a lot of emotional, intellectual and spiritual weight." In the film, Karamakate urges his Western passengers to throw their luggage out of their canoe, telling them they are "just things".  He wants them to get rid of a literal weight. "But the material is just a representation of the spiritual," says Guerra. "In the film it is visual, but I strongly believe the physical world is a reflection of your mind."

Embrace of the Serpent is playing at Palace Cinemas today and tomorrow