The area, covering 46,000 sq km (17,800 sq miles), straddles the northern states of Amapa and Para, and is thought to be rich in gold, and other minerals.
The government said nine conservation and indigenous land areas within it would continue to be legally protected.
But activists have voiced concern that these areas could be badly compromised.
A decree from President Michel Temer abolished a protected area known as the National Reserve of Copper and Associates (Renca).
Its size is larger than Denmark and about 30% of it will be open to mining.
