The National Institute for Space Research, known by its initials INPE, said that deforestation had cleared 870 square miles (around 2,250 square kilometers) of rainforest over the month.
The Brazilian president, a climate change skeptic, and his environment minister Ricardo Salles have previously accused the INPE of publishing misleading data, claiming the figures "don't correspond to the truth" and were damaging to the institute and the country.
Sharp rise in Brazilian deforestation undeniable, says sacked research chief
Data from INPE, an institution of international repute, shows that deforestation has increased 40 per cent in the last twelve months compared with the same period a year ago.
Amazon rainforest deforestation had increased 88 per cent on-year in June alone.
Last week, INPE president Ricardo Galvao was sacked following disagreements with Bolsonaro over deforestation in the Amazon, fueling criticism of the president from environmental groups.
The president suggested Galvao was "in the service of some NGOs" before dismissing him on Friday.
Bolsonaro was helped in his election last year by support from the powerful agriculture lobby.
He has previously floated the idea of opening up protected rainforest areas to agriculture, a highly controversial move given the existing level of deforestation.
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