But in a reversal of plot, there are now cases of people living traditional lifestyles who are now invading the territory of the big companies and taking them on at their own game.
The story of the Achuar tribe living in the Amazon rainforest of north-eastern Peru is one of them.
Last year, they filed a class action lawsuit against oil giant Occidental Petroleum, in Los Angeles.
Now they are awaiting a judge's decision on whether the case can proceed in the US or will be sent back to Peru, where it stands little chance of coming to court.
'No credible data
The Achuar people, who have lived for thousands of years in the rainforest, allege that the company contaminated their territory during more than 30 years of oil drilling, making their people sick, even causing some to die, and damaging their land and livelihoods beyond repair.
Occidental Petroleum, which pulled out of Peru eight years ago, denies liability in the case.
It has responded, saying: "We are aware of no credible data of negative community health impacts resulting from Occidental's operations in Peru."
The oil bonanza began in Peru almost 40 years ago when many foreign companies were given an open invitation by successive governments to test and drill in the Amazon.
What they did not consider was the devastating impact it would have on the native people, principally the Achuar - their land, their livelihood and their health.
The Achuar's spiritual leader, Tomas Maynas, wears a bright red headdress made of toucan feathers, and has red war paint streaked on his face. He is the plaintiff in the suit against the company.
He remembers how everything changed when the oil companies arrived. He says the animals ran away, the fish died and their crops started to wilt.
"The Peruvian state just wants to extract as much oil as they can from our land. They've made millions of dollars but we haven't seen it here.
"We know there's wealth here and there'll be more drilling so the state will keep on killing us. But sometimes, when there is pressure, the state gives in."
The lawsuit alleges Occidental Petroleum ignored industry standards and employed out-of-date practices, dumping around 9bn barrels of toxic waste water into streams and rivers over 30 years.
After Occidental left, its operations were taken over by Pluspetrol.
Pluspetrol agreed to change practices in late 2006 when the Achuar, after repeated attempts to negotiate, took direct action.
Shotguns and spears
Many of the older Achuar men once fought in tribal wars with their neighbours, now they finally had the chance to hit their elusive new enemies where it hurt - in their pockets.
Peacefully, yet armed with shotguns and spears, they occupied and held the Amazon oil wells in October 2006.
The government and the company, losing millions of dollars a day, were forced to come to the negotiating table.
The Achuar came away with a commitment from Pluspetrol to reduce contamination and to pay millions of dollars to clean up and establish a 10-year health plan.
It was thanks to help from outside but also a new generation of indigenous leaders who are learning how to protect their rights in the modern world.
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"A whole generation had their health damaged. How can we keep quiet as our parents did?" asks 29-year-old Petronila Chumpi.
"We can't allow this, we're a new generation, we know how to read and write and we have to help our people because they didn't have the knowledge to defend themselves against the oil companies. But now we do."
Even on a fast motorboat, Trompeteros is a long day's journey up three rain-swollen rivers from Loreto's regional capital, Iquitos. A hamlet of some 3,000 people, it is situated right opposite Block Eight, one of the main oil wells.
Local people say there is still contamination and oil spills, but now the Achuar have GPS transceivers to log the problems where they find them.
Little by little there are signs of improvement.
But there is frustration on the part of Pluspetrol, which has pledged to pay millions of dollars, that the government is not playing a bigger role.
"This oil industry should be of benefit for everybody - maybe today it's not of benefit to indigenous people and the government should find the best way to solve that problem," says Roberto Ramallo, general manager of Pluspetrol Norte.
But the problem is that the Achuar and other tribes live on top of potentially enormous reserves of crude oil.
Thanks to an intense drive to auction it off, almost three-quarters of the Peruvian Amazon is leased for oil exploration and extraction.
High global demand and the price of oil is also making companies look at the Peruvian Amazon as an attractive prospect, but is it sustainable?
"All of this petroleum exploration in the Amazon is a grand experiment," says Bill Powers of E-Tech, a not-for-profit engineering firm.
"It's just coming into the jungle, developing the resource, getting the economic benefit and historically it's been whatever happens to whoever was there before, happens.
"There's no plan, there's no effort made to ensure that they maintain their cultural integrity or that they have something to do once the rivers and the forest don't provide what they used to provide."
Carbon trading schemes have yet to reach this part of the Amazon and the oil boom is not the only threat.
President Alan Garcia has proposed privatising large areas of the rainforest, but local officials say the government in Lima does not understand the impact this would have.
The regional president of Loreto, Ivan Vasquez, says the Amazon needs to preserve its diversity at all costs.
"The ecosystem is the genetic bank of the Amazon, as it brings together genetic matrices which don't exist anywhere else - thousands of interconnected genetic bases.
"That is our capital, the genetic bank that we have to preserve for humanity, and for the world."
The Achuar have so far rejected new oil exploration on their territory.
Their story is an emblematic case of resistance for indigenous Amazonians and is unprecedented in Peru.
But the Peruvian rainforest, the biggest stretch of Amazon outside Brazil, is still the focus of the relentless global hunt to find new sources of fossil fuels.
© 2008 BBC News