Reuters exclusively accompanied raids by the Ibama environmental agency in the rainforest state of Para - the first since President Luiz Inacio Lula da Silva took power this month.
Lula has pledged to end surging destruction inherited from his predecessor, Jair Bolsonaro.
Other raids were launched over the past week in the states of Roraima and Acre.
This is the Cachoeira Seca indigenous reserve, where deforestation is strictly prohibited.
But illegal loggers and ranchers have cleared forest and destroyed unique flora including famous Brazilian ipe, or walnut tree.
Ibama agent David Belshoff:
"We are conducting an operation on this timber company. We had indications of irregularities and when we got here we confirmed that it was totally irregular. Now we're going to measure all the trunks of wood to make the seizure, issue an environmental fine and close the place down."
Most of the site appeared recently abandoned - which the agents said was down to Lula's pledge to enforce the law.
An area larger than Denmark was deforested under Bolsonaro, a 60% increase from the prior four years.
Bolsonaro's government targeted Ibama - gutting staff and funding, and criticising the fines it issued to farmers and miners.
Ibama was sidelined, despite its long experience, as Bolsonaro charged the military, and later the Justice Ministry, with tackling deforestation.
Lula vowed to put the agency back in charge with beefed-up funding and personnel.
"We need stricter laws and more personnel to fight them. Because we have often put pressure on a deforestation front and they quickly move to another location, so we need the logistics for the team to fight them anywhere."
Lula slashed Amazon deforestation by 72% during his last time in office from 2003 to 2010.
He was sworn in again on January 1, so additional money and staff have yet to reach front-line enforcers.
