The far-right president claimed “everything indicates” that charity groups were contributing to devastating forest fires in the region, which is a key carbon sink and home to millions of rare plant and animal species.
But he refused to back up his assertion the groups were attempting to bring shame on his government, saying he had “no written plan,” and adding “that’s not how it’s done”.
“Crime exists,” he said during a Facebook Live broadcast. “These people are missing the money.”
Brazil’s space research centre, Inpe, has detected 72,843 fires so far this year – an 84 per cent rise compared to 2018. The inferno has been blamed for a plume of smoke that blocked out the sun over Sao Paulo on Monday.
The state of Amazonas declared a state of emergency after a massive rise in the number and size of fires burning there.
Environmental groups have blamed Mr Bolsonaro for the devastation, saying he has encouraged the clearing of rainforest for logging and farming.
It comes after monitoring groups said deforestation in the Amazon had rocketed by 20 per cent in a year under Mr Bolsonaro, with uncontrolled logging and land invasion reportedly to blame.
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Mr Bolsonaro and his environment chief Ricardo de Aquino Salles have questioned the reality of climate change and backed the expansion of mining and industrial farming into the Amazon and protected regions.
The right-winger’s government is rolling back enforcement measures like fines and the seizure or destruction of illegal equipment.
Earlier this month, the former director of Inpe was sacked after the agency released data showing a rise in deforestation that Mr Bolsonaro later derided as “lies”.
Additional reporting by agencies