To the village of Copal Urco, home to a few hundred indigenous Kichwa farmers and fishermen near Peru's border with Ecuador, uncontacted tribes are no myth. They themselves were uncontacted once, until European missionaries and soldiers sailed up their river, and they say such groups still live deeper in their forest. Some are thought to have had brief contact with outsiders decades ago during the rubber boom but then, frightened or repulsed, retreated. They have mostly covered their tracks since, says Roger Yume, 38, the village apu, or chief. "We have seen the signs." Footprints, tracks through foliage, occasional glimpses of fleeting figures - there is no doubt. "They exist. Our brothers exist."
Not everyone agrees. The existence of uncontacted tribes in Brazil and Ecuador is accepted, but Peru's government has ridiculed the notion of such communities in its part of the Amazon. President Alan Garcia says the "figure of the jungle native" is a ruse to prevent oil exploration. Daniel Saba, former head of the state oil company, is even more scornful. "It's absurd to say there are uncontacted peoples when no one has seen them. So, who are these uncontacted tribes people are talking about?"
It is an urgent question. Peru, home to 70m hectares of Amazon, second in size only to Brazil, has parcelled up almost three-quarters of its rainforest for oil and gas projects. Of 64 exploration blocks, known as lots, all but eight have been created since 2004. "The Peruvian Amazon is now experiencing a huge wave of hydrocarbon exploration," says Matt Finer, co-author of a study of oil and gas projects in the western Amazon by Duke University and Save America's Forests.
Oil extraction is not subtle. It involves helicopters, barges, road clearance, drilling platforms, wells and pipelines. Technology is cleaner than before but still pollutes waterways and frightens game. And the workers still bring germs, which threaten tribes with no immunity to outsiders' diseases. Flu and other ailments brought by conquistadors wiped out much of Latin America's indigenous population, and more recent interlopers - loggers, missionaries, scientists and journalists - have wrought deadly consequences in isolated communities. After incursions by oil men into Nahua territory in the 1980s, more than half the tribe reportedly died. "If companies go in, it's likely to destroy the Indians completely and then they really won't exist," says Stephen Corry of the advocacy group Survival International.
Even oil companies admit their presence would have serious implications for uncontacted tribes. The question is: are there any? If so, by law, the exploration should be halted or at least heavily circumscribed. That would impede Peru's hopes of becoming a net oil exporter - a windfall that could go a long way in an impoverished nation of 28m. Social anthropologists say that would be a small price for preserving humanity's rich mosaic.
The frontline of this existential battle is Lot 67. A swath of jungle in the Maranon basin in north-east Peru, it comprises the Paiche, Dorado and Pirana oilfields, which contain an estimated 300m barrels - a geological and commercial jackpot. An Anglo-French company, Perenco, holds exclusive rights. It plans to spend $2bn - the country's biggest investment - drilling 100 wells from 10 platforms. The crude will be shipped and piped 600 miles to the Pacific coast. Extensive seismic testing has been conducted and installations built. Barges await the first barrels.
To settled indigenous communities such as Copal Urco, this spells death to their "hidden brothers". They say there are three uncontacted tribes in Perenco's area, the Pananujuri, Taromenane and Trashumancia. Peru's indigenous umbrella group, Aidesep, estimates their joint population at 100. Stories about sightings are passed up and down the Napo river. Denis Nantip, 22, says his uncle encountered one group in 2004. "He was deep in the forest with a logger. They were bathing in the river and suddenly saw people staring at them. They had spears and leaves with string covering their genitals." The two intruders were left unharmed but loggers never dared venture back to that part of the forest.
Perenco, echoing Peru's government, dismisses these claims as rumour and misinformation by groups opposed to economic development. "This is similar to the Loch Ness monster. Much talk but never any evidence," says Rodrigo Marquez, Perenco's Latin American regional manager. "We have done very detailed studies to ascertain if there are uncontacted tribes because that would be a very serious matter. The evidence is nonexistent."
A team of investigators - anthropologists, biologists, linguists, historians, archaeologists, forestry engineers - combed Lot 67. They looked for footprints, dwellings and spears. They looked for animal traps, paths, patches of cultivation. They asked the Arabella tribe, which has been in intermittent contact with the outside world since the 1940s, about recent sightings or evidence. They analysed Arabella speech patterns and oral histories for clues. Result: nothing. No compelling evidence, no compelling indications. The 137-page final report concludes that if there were uncontacted tribes, they were long gone, either dead or in Ecuador. The findings opened Lot 67 to an oil deal which the government declared to be in the national interest. "All these studies have shown there is no trace at all," Marquez says.
Not everyone is convinced, however. Tracking uncontacted tribes, it turns out, is a detective story within a detective story.
Iquitos, reputedly the world's largest town inaccessible by road, is a sultry, humid outgrowth of the rubber boom, a bustle of oil men, backpackers, missionaries, traders and prostitutes perched by the Amazon river. By the docks, on Avenida La Marina, there is an office stencilled with the word Daimi and a rainbow logo. It is a consultancy that carries out environmental impact assessments (EIAs) for oil companies, a mandatory requirement for government authorisation to explore and drill. They can make or break a company's bid to drill, and shape the regulations under which they operate. Daimi, plucking scientists from different institutions, has done studies for eight companies besides Perenco, including Argentina's Pluspetrol, Brazil's Petrobras, Canada's Hunt, Spain's Repsol and the US's Oxy.
Oil companies pay for EIAs and insist that the reports are independent and impartial. Within the NGO and academic community, there are some who have long claimed they are not. But there is nothing concrete, and it is difficult to investigate since even those with university tenure often rely on EIA commissions to supplement meagre salaries.
Virginia Montoya sits in her office, maps and books piled on her desk, and lets the question hang in the air. The silence stretches to a few seconds. She is a director of the Institution for Research on the Peruvian Amazon, a senior anthropologist and champion of indigenous women's rights. She was also a consultant on Daimi's report. Does she think there are uncontacted tribes in Lot 67? Montoya fidgets, then takes a decision. "Yes. Yes, I do." She hesitates once more. "There is no doubt in my mind that there are uncontacted groups there." She says she had documented evidence, especially pathways. "I was really upset when I saw the final report. It didn't lie, the language was technically correct, but it did not reflect my view."
On the other side of Iquitos, on a rutted road of colourfully painted houses, there is the same long pause before Teudulio Grandez answers the same question. An anthropology professor at the National University of the Peruvian Amazon, he was cited as a lead author in the Daimi report. A portrait of Che Guevara looks down from the wall as he wrestles with his answer. Finally, it comes out. "Yes. Certain nomadic groups are there. Our conclusion is that there are." He exhales deeply.
And then, in another part of Iquitos, a third voice. Lino Noriega, a forestry engineer, participated in eight missions to Lot 67 to investigate the impact of seismic tests - small explosions that cleared strips of forest and probed the soil. (He has since left Daimi following a contractual dispute.) "They said there were no uncontacted groups. But there were footprints, signs of dwellings."
There is no single smoking gun in the three testimonies. The allegations were put to Daimi, but they were unable to put forward anyone to respond. Perenco's regional manager, Marquez, defends the EIA research. "These are just opinions. These scientists need to produce evidence. We have gone to tremendous effort to put these reports together in the most professional way. It's easy to build conspiracy theories."
EIAs are vetted by several government departments. "We are committed to environmental protection. We don't want these reports to be wishy-washy," says the foreign minister, Jose Antonio Garcia Belaunde. He promises to look into the Lot 67 allegations.
Critics say the environment ministry has little clout against more powerful departments driving the oil rush. Peru's government is not impartial and does not encourage genuinely independent EIAs, says Jose Luis de la Bastida, a Peru oil specialist at the Washington-based World Resources Institute. Last year the energy minister and head of state oil company PetroPeru resigned amid a scandal over alleged kickbacks from a Norwegian oil company to the ruling party. They denied any wrongdoing. There is also unease over the revolving door between oil companies and government. "A lot of overlap, it's an old boys' network," says Gregor MacLennan of advocacy group Amazon Watch.
Lima is, and feels, a long way from the Amazon. A sprawling coastal capital of eight million people ringed by slums, its downtown has Starbucks, shiny skyscrapers, smart government offices and some of South America's best restaurants. Historically it has looked outwards to the Pacific ocean and seldom thought about the 300,000 dark-skinned "nativo" forest-dwellers, little more than 1% of the population. It has had even less reason to ponder uncontacted tribes. There was little dissent last year when President Garcia decreed laws carving up the Amazon for oil, gas, mining and biofuel projects.
The "nativos", however, rose up. Scattered, impoverished and marginalised, they organised protests against what they said were land-grabbing polluters who poisoned their soil and rivers. They blocked pipelines, roads and waterways. The president denounced them as "ignorant" saboteurs and last month ordered security forces to lift the blockades. In the town of Bagua, mayhem erupted. Officially, 24 police and 11 protesters died. Indigenous groups say there were dozens if not hundreds of civilian casualties and that bodies were burned and dumped in rivers - claims the government denies.
Garcia, realising he had misjudged indigenous wrath and strength, revoked two of the most controversial decrees, 1090 and 1064, which would have opened the Amazon to biofuel plantations. Indigenous groups suspended the protests but oil and gas projects are still going ahead. "The future scenario remains terrifying. The Peruvian Amazon is still blanketed in concessions," says Finer, co-author of the Duke study.
There are two views about what happens next. Brother Paul McAuley, a British Catholic lay missionary, teacher and pro-indigenous activist in Iquitos, believes a flame of resistance has been lit. He sees it in his civil association, Red Ambiental Loretana. Indigenous communities are organising, plotting their next move. "I think they're going to win this." The 61-year-old's mild manner belies a combative streak which has earned him death threats and a "terrorist" label from pro-government media. Had he not already given it away, he would have returned his MBE (for services to education in Peru) in protest at what he sees as Britain's complicity. He hopes the Amazon's "spiritual force" will mobilise western public opinion against the oil companies. "More than its oil, what the west needs is the Amazon's spiritual energy."
The fatalistic view holds that it'll take a miracle, divine or otherwise, to stop the drilling. Wells are being dug, pipelines laid, profits calculated. Oil companies and the Peruvian government are committed - especially to the great prize that is Lot 67. Jack MacCarthy, a US surgeon and Catholic missionary who has spent 23 years in the jungle, believes the die is cast. "If Perenco doesn't drill, someone else will. I don't think there's any way to keep that oil in the ground. There are enough powerful and rich people in the world who want it. And they'll get it, regardless of the cost."
In which case, if there are uncontacted tribes in Lot 67, their fate may be to disappear - definitively - and join the legends of the Amazon.
• See Rory Carroll and Marc de Jersey's film about the Peruvian Amazon at guardian.co.uk/video