Representatives of 14 indigenous groups and four riverside reserves in the basin met in the Kubenkokre village last week.
Forest fires, thought to be deliberately started, are currently ravaging the Amazon, with critics blaming Jair Bolsonaro’s government for encouraging people to clear the land for farming, logging and mining.
The landmark meeting of indigenous communities was hosted by the Kayapós group, one of the largest communities in the river basin, according to BBC Brazil.
“Today we have only one enemy, which is the Brazilian government, the president of Brazil, and the invasions of non-indigenous people,” Mudjire Kayapó, one of the leaders present, told the broadcaster.
“We have internal fights, but to fight this government, we join.”
The participating communities have decided to form a representative council, to strengthen their collective political voice.
The Kayapós invited representatives of the Panara people to the meeting, despite the two groups having fought violently in the past.
The Kayapós notably massacred the Panaras in 1968, during a fight in which they used firearms despite the latter tribe being armed only with arrows.
“We killed the Kayapó, the Kayapó killed us...but we didn’t know what was happening....we didn’t know about that [white] threat yet,” said Sinku Panara, one of the Panara leaders.
“Then we cool our heads, reconcile, talk to each other again and we will not fight anymore.
“Because there is a common interest for us to fight together, so that non-Indians don’t kill us all.”
Mr Bolsonaro’s poll ratings have fallen rapidly since the Amazon fires took hold, according to the Datafolha polling institute – the number of people who think the far-right leader is doing a “bad or terrible” job rose to 38 per cent from 33 per cent in July, as his government’s handling of the surging fires divided the country.
The president campaigned on numerous culture war issues, including bringing development to the rainforest.
As Brazil struggles through a prolonged economic stagnation, the allure of the Amazon has grown, even as scientists warn that development will accelerate rising deforestation.
On the day after his inauguration, Mr Bolsonaro decried the fact that 15 per cent of Brazil’s territory is reserved for indigenous tribes.
“Let’s integrate these citizens and bring value to all Brazilians,” he tweeted.
It’s estimated that nearly 50,000 Amazon blazes have ignited this month alone, 89 per cent more than in August 2018 on a scale not seen since 2010.
The devastating fires have prompted global concern over the Amazon, which provides 20 per cent of the world’s oxygen supply.
The largest rainforest in the world, it is vital for slowing down the pace of global warming.
Mr Bolsonaro has dismissed global worries over the fires and has insisted the blazes are under control.
On Monday the 64-year-old pulled out of a regional summit which he had convened to discuss the impact of the fires.
Mr Bolsonaro said he would not be attending the meeting, which will be held in Colombia on Friday, because of an upcoming surgery to treat a hernia.
The politician was stabbed in the abdomen during the presidential campaign.
He said he would be willing to discuss the fires at the next UN General Assembly in September.
“I will appear before the UN even in a wheelchair, on a stretcher,” he claimed.
”I will appear because I want to talk about the Amazon.”
Additional reporting by agencies
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