The Mapuche are suing American giant Exxon, French company Total and the Argentina-based Pan American Energy, which is part owned by BP.
Two more Argentine oil and gas companies -- YPF SA and Pampa Energia -- are named in the lawsuit, along with the local Neuquen province authorities and Treater, a local company operating a treatment plant for fracking waste.
The Neuquen Mapuche Confederation accuses the oil and gas companies of harming the environment with "dangerous waste" due to "deficient treatment" close to the town of Anelo, some 1,200km (750 miles) south of the Argentine capital Buenos Aires.
"It's quite a sensitive situation," Martin Alvarez, an expert with the Observatorio Petrolero Sur charity that monitors energy use, told AFP.
"It's affecting the inhabitants of popular neighborhoods because the waste treatment plants are too close."
Following an investigation, Greenpeace published a report in which it accused Total and British-Dutch group Shell -- which does not figure in the Mapuche lawsuit -- of dumping "highly toxic oily sludge waste."
It claimed that the residue from fracking "is being tipped in illegal waste dumps, causing massive pollution that threatens wildlife and human health" in Patagonia.
The waste comes from exploitation of the Vaca Muerta site in Neuquen, one of the biggest shale-oil and shale-gas deposits in the world.
Patagonia is a sparsely populated and ecologically rich area that spans around 400,000 square miles (one million square kilometers), mostly in Argentina but also partly in Chile.
Much of the area is taken up by protected national parks.
Greenpeace said it found the dumps in November last year and started taking samples from them in May.
It said it had tracked trucks dumping waste to two sites, one linked to Shell and the other to Total.
The dumps, including one which has grown to the size of "almost 15 football fields," are located just three miles from Anelo, Greenpeace said.
While Shell is not named in the lawsuit, it signed a deal in 2017 with Argentine state-run oil company YPF SA to develop oil and gas assets in the Vaca Muerta shale field, a site of some 11,600 square miles.
A Pan American Energy spokesman told AFP that its name featured in the lawsuit by mistake as it doesn't have a contract with Treater, which operates the waste plants.
On its website, Treater identifies Pan American Energy -- whose other partner, Argentine company Bridas, is 50 percent owned by Chinese giant CNOOC -- as one of its clients.
None of the other companies named in the lawsuit commented.