Agents fired automatic weapons at motor boats carrying fleeing miners from their helicopter.
They fired again to blow up barrels of diesel fuel and set fire to excavators so they could not be used again.
A handful of wildcat miners were detained.
The miners had cut down swathes of jungle and dug dozens of ponds to dredge for gold.
Sidney Serafim is the mission commander for the three-week operation.
"We have more than 20 illegal miners and more than 20 clandestine airstrips located here."
Serafim added that even after law enforcement destroyed miners' camps, they keep coming back.
Leftest President Luiz Inacio Lula da Silva's government has already been cracking down on mining on Indigenous lands.
But that has pushed some miners to other forests where there has been little enforcement.
Lula has vowed to stamp out illegal mining and end deforestation by 2030.
That's a sharp reversal of policy from his predecessor Jair Bolsonaro who was criticized globally for relaxing environmental controls as well as giving illegal loggers and miners free range in the Amazon.
He argued that Brazil had the right to develop its natural resources.
In the mission Serafim led, the detained miners were set free into the jungle on foot.
Only the manager of one of the wildcat mining sites was taken into police custody.
