Deforestation is a key factor behind global warming, accounting for around 15 per cent of annual emissions of heat-trapping gases, similar to that of the transportation sector.
Brazil's environment minister Edson Duarte said that illegal logging was the main factor behind the increase in deforestation in the Amazon.
He called on the government to increase its policing of the jungle.
Brazil's Climate Observatory, a network of non-governmental organisations, said that the increase also caused by Brazil's growing commodities sector as farmers sought to expand.
Marcio Astrini, from the local office of Greenpeace, said the Brazilian government had not done enough to fight deforestation and recent policy moves such as ones reducing areas under federal protection fuelled environmental destruction.
Both groups said they were worried that deforestation could increase further during the government of President-elect Jair Bolsonaro, due to take office in January.
He has sharply criticised the Brazilian environmental protection agency, and the agriculture sector is one of his main political bases.
Despite the recent rise, deforestation remains sharply below the levels recorded in the early 2000s, before the Brazilian government launched a strategy to fight forest destruction.
In 2004, for example, more than 27,000 square km were cleared, an area the size of Haiti.
Scientists consider the Amazon as one of nature's best protections against global warming, as it acts as a giant carbon "sink" by absorbing the gas.
The jungle is also rich in biodiversity, hosting billions of species yet to be studied.