Last year, there were 32.3 homicides per 100,000 inhabitants in the vast rainforest region, compared with a nationwide rate of 22.8 -- a 41.5-percent difference, according to the study by the Brazilian Forum on Public Security (FBSP).
In all, there were 8,603 killings recorded in Brazil's Amazon in 2023, it said.
The NGO said it had drawn a direct correlation between the opening of roads in the Amazon, and stepped-up economic activity, with an increase in violence.
Organized crime present was drug trafficking, as well as illegal logging and other illicit environmental businesses, it said.
"This control goes through chains of production, including cattle-raising in state land taken by land-grabbers, illegal logging, predatory fishing and, mainly, mining on Indigenous land," FBSP director Renato Sergio de Lima said.
The struggle to control tracts of land "occurs in violent ways" and "connects all the main criminal activities" in the Amazon, he said.
The Amazon rainforest -- whose survival is crucial to slowing the pace of global warming -- accounts for 59 percent of Brazilian territory, where it covers five million square kilometers (1.9 million square miles).
More than half of Brazil's Indigenous population lives in that region.
The FBSP study identified criminal groups in a third of the Brazilian Amazon's 772 municipalities -- areas in which 83.7 percent of the homicides occurred.
One of Brazil's biggest crime organizations, the Comando Vermelho (meaning "red command") dominates half of those communities, the study said.
Another 28 are controlled by a rival outfit, the Primeiro Comando da Capital ("capital's first command"), while 85 are being fought over or are prey to multiple groups.
While the FBSP study noted a small reduction of 6.2 percent in lethal violence over the period 2021-2023 compared to the previous three-year span, its researchers said that did not substantially change the overall picture for violence.
Brazilian President Luiz Inacio Lula da Silva's government in June launched a plan to boost state security forces in the Amazon.
Outside monitoring of illegal activities harming the Amazon environment was last month given as the reason for the 2022 double murder of a British journalist, Dom Phillips, and a Brazilian Indigenous expert, Bruno Pereira.
Federal police concluded that the two were shot dead in a remote Indigenous reserve because of Pereira's monitoring of poaching and other illegal activities going on in the Amazon.
Phillips, a 57-year-old freelancer for The Guardian and The Washington Post, had been traveling with Pereira to research a book he was writing about the rainforest.
Their hacked-up bodies were found days after their disappearance. Autopsies showed they had been shot with shells used for hunting.
Several people accused of illegal fishing and drug trafficking in the region were arrested over their murders.
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