The National Institute for Space Research (INPE) said 312.6 square kilometers (120 square miles) were destroyed in June, based on the preliminary analysis of satellite photos of the vast South American rainforest.
May had seen a decrease in deforestation to 268 square kilometers (100 square miles) from 477 square kilometers (180 square miles) in April.
In April, more than 400 square kilometers (150 square miles) of forests were destroyed in a single state, Mato Grosso, which is seen as a major agricultural frontier and is used for cattle ranches and soybean farming.
At the 2009 UN climate change summit in Copenhagen, Brazil committed itself to reducing Amazon deforestation by 80 percent by 2020.
Brazil, the world's fifth largest country by area, has 5.3 million square kilometers of jungle and forests -- mostly in the Amazon river basin -- of which only 1.7 million are under state protection.
The rest is in private hands, or its ownership is undefined.
Massive deforestation has made Brazil one of the world's top greenhouse gas emitters, and the pace of deforestation peaked in 2004 at 27,000 square kilometers (10,000 square miles) a year.
By 2010, however, it had dropped to 6,500 square kilometers, thanks in part to the INPE's Real-Time Deforestation Detection System (DETER), which allows researchers to collect new satellite images on a daily basis.
However, the system can only monitor areas of 25 hectares (60 acres) or more, so its results are not considered definitive.