The report lays bare the destruction of an ecosystem often referred to as the lungs of the Earth.
"At least 36 per cent and up to 57 per cent of all Amazonian tree species are likely to qualify as globally threatened," said the study in the journal Science Advances, which used criteria from the respected International Union for Conservation of Nature (IUCN).
Under a business-as-usual scenario, about 40 per cent of the original Amazon forest would be destroyed by 2050, the researchers found. But with stricter conservation measures, they said, that number could be halved.
The good news is that significant populations of endangered trees survive in protected areas of the Amazon, the researchers said.
Still, they added, only constant vigilance over valuable trees like the Brazil nut - 63 per cent of which could otherwise be lost by 2050 - will help preserve the Amazon's status as a major carbon sink.
The report was based on forest surveys across the Amazon and maps of current and projected deforestation. Researchers from 21 countries contributed.
"Either we stand up and protect these critical parks and indigenous reserves, or deforestation will erode them until we see large-scale extinctions," said lead author Hans ter Steege of Naturalis Biodiversity Centre in the Netherlands.