Satellite data for a 12-month period ending in July 2013 showed deforestation in the region increased by 28 percent compared with a year earlier, driven largely by expanding farms and clearing of land around big infrastructure projects.
A total of 2,250 square miles of land was cleared during the period.
Scientists and environmentalists have been warning destruction was on the increase after progress in slowing it in past decades.
"You can't argue with numbers," Marcio Astrini, coordinator for the Amazon campaign at the Brazilian chapter of Greenpeace told Britain's The Guardian. "This is not alarmist -- it's a real and measured inversion of what had been a positive trend."
High global prices for agricultural commodities have led to a push by growers to cut trees to increase farm yields, while changes to Brazil's forestry laws have created uncertainty among landowners about the amount of woodland they must preserve.
Izabella Teixeira, Brazil's environment minister, dismissed criticism that government policies had led to the increase in deforestation. The government's goal, she said in the capitol Brasilia, was "to eliminate illegal deforestation in the Amazon."
The overall trend was "positive," she said, citing the long-term decrease in forest loss in the last 10 years.