The study, which will cost around $33 million (U.S.), is expected to be completed in four years.
Environment Minister Isabella Teixeira signed an agreement with the National Development Bank, which plans to fund the census.
The government says that the inventory will play a key role in developing policies that will slow the destruction of the Amazon.
Last year, Brazil lost 4,656 square kilometres of the Amazon to deforestation.
More than 60 percent of the Amazon rainforest is located in the country.
With files from the Canadian Press