"The jungles of Brazil are at a breaking point," said Professor Britaldo Soares-Filho, co-author of the study.
A fifth of Brazil's soy and beef exports to the European Union come from illegally deforested land, according to research published in the journal Science.
The report, entitled "The bad apples of the Brazilian agribusiness", comes amid a strong resistance in Europe to the ratification of the free trade agreement signed last year between the EU and Mercosur, the South American trade bloc including Brazil.
According to official data, 3,070 km2 of the Brazilian Amazon was burned or chopped down between January and June this year, up 25% from the same period last year. The report also points to the "European appetite" as being responsible.
In the last two decades, Brazil, the world's largest soybean producer, has quadrupled its grain production and is expected to increase another third in the next 10 years.
Pig farmers in the European Union, the world's largest exporter of this meat, are also dependent on Brazilian soybeans, due to the growing demand for pork in Asia and other regions.