In the seventeenth century slave trader Pedro da Costa Favella, with an army of soldiers and "civilized Indians," massacred and enslaved Indians on the Rio Urubu, to the south of the present-day territory of the Waimiri-Atroari. There are reports of eighteenth-century expeditions to capture Indian slaves, together with missionary activity on the Rio Jauaperí. Attempts to settle the Indians of this river continued in the nineteenth century. Many documents from the mid-nineteenth century reveal a long history of interethnic conflicts. The provincial government organized punitive expeditions in which hundreds of Indians were massacred. In 1884 Barbosa Rodrigues (1885) established nonviolent relations for a short time with the Indians of the Rio Jauaperí and tried to pacify them. After more conflicts and massacres of Indians, Alipio Bandeira reestablished nonviolent contact in 1911, indicating that the initiative for violence always came from the non-Indian population.
The Indian Protection Service (SPI) founded an Indian post on the Rio Jauaperí, where many Indians died from epidemics. After land invasions, the post was moved upriver. The new post was invaded and destroyed, however, by a gang of armed Brazil-nut gatherers led by a trader with support from the local government. The SPI abandoned the post and in the 1940s established posts on the Rio Camanaú, which were destroyed several times by the Indians. Invasions of their territory forced the WaimiriAtroari to retreat to the headwaters of their rivers. In 1968 FUNAI started an intensive campaign to "attract" the Waimiri-Atroari to Indian posts, in conjunction with those constructing the BR-174 highway between Manaus and Boa Vista; the Waimiri-Atroari Indian Reserve was created in 1971. The FUNAI "attraction front" directly confronted the Indians, who were situated between them and the gangs of road builders from the army and construction companies. The Indians, after indiscriminate contacts with soldiers, laborers, and FUNAI workers, suffered lethal epidemics of Western diseases, which wiped out entire villages. In their struggle to combat what they believed to be attacks of sorcery, and in view of the mass deaths, they attacked other Waimiri-Atroari villages and made several attacks against FUNAI posts.
The indigenist policy in this area was directed by the army, which recommended the use of force to frighten the Indians. The Waimiri-Atroari population was drastically reduced within the space of a few years; the survivers were settled at FUNAI posts between 1978 and 1983. They were subjected to a rigid regime, directed by a large contingent of FUNAI workers and forced to work on imposed projects aimed at reorienting their lives to attend to the ecomomic interests of the federal government. The FUNAI "attraction front" imposed drastic transformations on their way of life in an attempt to resocialize them as sedentary agriculturists. During these years many more Wairmir-Atroari died in epidemics, often in consequence of omissions by FUNAI.
Beginning in 1979, the Paranapanema Mining Company invaded Waimiri-Atroari territory. After a series of cartographic manipulations in which the name of the upper course of the Rio Uatumã was changed, in 1981 a presidential decree dismembered about one-third of Waimiri-Atroari territory to favor Paranapanema, thereby canceling the Indian reserve and turning what remained into a "temporarily prohibited area." In 1982 the mining company encroached again, constructing a private access road linking the BR-174 highway to the dismembered area. FUNAI authorized the highway's construction after it had already been started. In 1987 about one-third of the Waimiri-Atroari population was transferred from the headwaters of the Rio Abonari because the river had been transformed into a huge putrid lake of flooded forest by the Balbina hydroelectric scheme. This was the same area that had been disappropriated from the reserve by decree in 1981. In 1987 an agreement was signed between FUNAI and ELETRONORTE to finance an aid program aimed at the Waimiri-Atroari. The Waimiri-Atroari Program now administers the indigenist policy in the area.
Despite the demarcation and homologation of the Indian area in 1989 and the subprograms that focused on providing assistance in health, education, and environment and production, the pressures exerted by big companies continued. From 1986 Mineração Taboco (Paranapanema) started enticing the young Waimiri-Atroari "captains," trained and appointed by FUNAI as intercultural agents, to sign inequitable agreements accepting economic projects, including cattle raising, in exchange for permission to occupy more of their territory. In 1987 five captains signed an agreement with Paranapanema and FUNAI that allowed the mining company to advance over the entire Indian territory in exchange for royalties. In 1989 ten captains, together with FUNAI employees, signed an agreement to receive advance monthly royalty payments for mining activities that Paranapanema planned to undertake within the Indian territory.
At the same time, a plan using forged documents was set up as an incentive to the Waimiri-Atroari to ban the continuation of an ethnological research proposal. The document "showed" the Indians that the ethnologist was an agent of a supposed "tin cartel" that was using Indians to try to prevent the Paranapanema Mining Company from advancing over Indian territory, purportedly to favor international tin-mining interests. This marked another step in a long series of irregular procedures that this mining company, together with FUNAI, have been using against the Waimiri-Atroari.