The first blow was enough to kill Sobral Magalhaes, sending his eyeballs popping out of their sockets. The second blow mashed his skull to a bloody pulp. His assailants were club-wielding Indians from the Korubo tribe, known — and feared — throughout this remote area of western Brazil as the caceteiros: head-bashers.

"They weren't to know we were trying to help them," said Sydney Possuelo, the Amazon's leading Indian tracker, and the dead man's friend and colleague for almost 20 years. "To them we look the same as the loggers and gold-miners and adventurers who have been terrorising them for centuries. They were simply defending the territory they always considered theirs."

Passing the darkly forested banks of the Itui river where Sobral was killed, Possuelo switched off the motor of his boat and we drifted on the cappuccino-coloured water. The still air was suddenly rent by screeching monkeys and peals of thunder. Possuelo pointed to the spot where he had erected a cross for his friend. "This is a bad place. Last year a six-year-old Korubo girl was killed by an anaconda in exactly the same spot."

Coming under attack by head-bashing Indians or 20ft-long anacondas is all in a day's work for Possuelo, who heads Brazil's Department of Isolated Indians — a division of the country's Indian Protection Service (Funai) — whose motto is "Die if you must (but never kill)".

This real-life Indiana Jones is the last of the Amazon's great sertanistas, those sent into one of the last uncharted places on Earth to "open up" the interior and find tribes such as the Korubo, who have had no interaction with "civilisation". Now 64, he has had malaria 39 times; been kidnapped by Indians for 28 days; narrowly escaped poison arrows; lived for days on laxative acai berries; slept for nights on hammocks invaded by crab spiders; had his front teeth punched out by ranchers; survived plane crashes (one of which destroyed the small aircraft given to him by the king of Spain) and car crashes (the most recent resulted in a metal plate in his skull).

He receives death threats, and his legs are speckled black with bites from bloodsucking pium flies. He looks the part of the rugged explorer, too: wild-eyed and wild-haired under a floppy camouflage hat, with a straggly beard and bare feet as splayed as those of the tribespeople he tracks. An unabashed romantic, he strides through the Amazon singing bossa nova and quoting Somerset Maugham. He also has the shortest of tempers and his personal life is a disaster (he has had three broken marriages, and his own mother calls him a mulherengo: an incorrigible womaniser).

No living explorer has made contact with more tribes. This year he was awarded the Royal Geographical Society's gold medal, joining the ranks of 19th-century legends such as Sir Richard Burton, John Hanning Speke and David Livingstone. Possuelo once thrived on the business of tracking Indians, leaving gifts hoping to entice them out, in the same manner as the missionaries of old. But after 40 years as a sertanista, he now thinks they should be left alone.

On this trip we were hoping to meet two of the tribes he is trying so fiercely to protect. We started out in the steamy jungle town of Santarem, where the Amazon river meets the Tapajos. After medicals to ensure we weren't carrying any infectious diseases, including the common cold, we squeezed into a single-engine Beechcraft and flew north, over a new soya port, which set Possuelo off, grumbling about deforestation.

In today's interconnected world it is hard to imagine that there could still be communities who have never seen a wheel, switched on a light, or become aware of the European colonisation of the Americas. Hard to imagine, that is, until you fly over the rainforest. For hours you see nothing but jungle and the occasional brown river snaking back and forth. Brazil is the size of western Europe, and over half of it is covered by the Amazon. The Brazilian explorer Euclides da Cunha called it "the last page of Genesis".

The area is thought to shelter the world's largest number of uncontacted tribes. At least 20 groups are unchanged from Stone Age times. They live naked and hunt with bow and arrow, just as they did in 1500, when the Portuguese explorer Pedro Alvarez Cabral landed in Brazil. Their settlements have been seen from the air or by satellite imagery, and there have been sightings by biologists and others venturing into remote regions. "We don't know how many groups there are," said Possuelo. "We have reports of about 42, of which 17 have been confirmed. But it's slow work and costly in terms of money and lives."

Funai was set up in 1910 to make contact with these "wild" people and assimilate them into society — and pave the way for development of the Amazon with roads, dams and mines. After years working in these so-called "attraction fronts", Possuelo is now trying to turn the agency's mission around: "These are people who said they don't ever want to see whites again; perhaps they are survivors of massacres, so have fled into the remotest corners of the jungle, and we should respect that. The history of our treatment of Indians since the Discovery is a terrible drama of torture, death and blood in the name of progress or religion."

The numbers bear him out. When Europeans first reached Brazil about 500 years ago, the indigenous population was an estimated 5m to 7m. Today it is around 350,000. Yet the "terrible drama" to which Possuelo refers is not just the colonial massacres of long ago. Rather than benefiting from the technological and medical advances of our world, Indians continue to be destroyed by its temptations, such as alcohol, or killed by those who covet their lands and resources.

During the past 100 years, even well-meaning whites wiped out tribe after tribe by bringing in illnesses against which the Indians have no defences: chickenpox, measles, influenza and tuberculosis. According to the anthropologist Darcy Ribeiro's book Indians and Civilization, 100 Indian tribes disappeared in Brazil between 1900 and 1970, the year his work was published. Possuelo insists more have been lost since. "Each time we have lost 30%, 40%, 50% of a tribe or seen it wiped out, it's been regarded as the acceptable norm. Well, I don't think that it is."