When archaeologists Eduardo Kazuo and Márjorie Lima recently unearthed nine pre-Columbian funerary urns in Tauary – a tiny community in Brazil’s Amazon rainforest – their immediate reaction was “a mix of pleasure and desperation”.

The bulbous vessels – containing human remains and writhing with anthropomorphic painted serpents and monkeys – are the only ones of their kind to be excavated intact.

But the extraordinary find last year underlined the precarious situation of the small team at the Mamirauá Institute for Sustainable Development which found them.

Reliant on international funding, they are the only archaeologists for 500km in every direction. “We need students, researchers, money,” said Kazuo. “And now we have the government that we have …”

Recent findings are radically changing our understanding of the region’s prehistory. New evidence suggests that pre-Columbian Amazonian civilisations were comparable in scale and complexity to better-known Andean and Mesoamerican cultures. They had populations numbering in the millions, living in interconnected, fortified villages. They left rock art, vast ceremonial earthworks, sprawling irrigation channels and causeways, but any stone buildings, described in fanciful accounts by conquistadors, have not survived. Perhaps even more intriguingly, a growing body of research suggests that much of the world’s largest rainforest was moulded by humans.

But archaeologists across the Amazon warn that progress is imperilled by the policies of Brazil’s nationalist president, Jair Bolsonaro. The field is facing dramatic funding cuts, while proposed legal changes on salvage archaeology will endanger priceless physical evidence.

And the mass displacement of indigenous communities – resulting from Bolsonaro’s promises to turn the Amazon over to loggers, miners and farmers in the name of development – risks destroying the local knowledge needed to reconstruct the Amazon’s past, and potentially safeguard its future.

“It’s a great time to be doing archaeology, but it’s threatened,” said Eduardo Neves, a professor at the University of São Paulo (USP) and the doyen of modern Brazilian archaeology. “Science and higher education in Brazil are under a major cloud … The whole outlook is pretty bleak.”

A view of Tauary community, where ancient urns were found in late July. Photograph: Jessica dos Anjos Oliveira

In Rondônia, western Brazil, Eduardo Bespalez and Silvana Zuse – archaeologists at the state’s federal university UNIR – squeezed through thick foliage.

On both sides of the trail rose huge banks of terra preta, or Amazonian dark earth: dense, fertile soil, produced from ancient cooking fires, rubbish and farming. Spongy to the touch, the black dirt was studded with fragments of pre-Columbian pottery to several metres’ depth.

Rondônia – now one of Brazil’s most deforested states –was once a crucible of South American civilisation. This site, known as Teotônio, displays “some of the deepest, oldest and most fertile terra preta in the Amazon”, said Bespalez, with some deposits 7,000 years old.

Ancestors of the Arawak, Tupi-Guarani and Pano linguistic groups overlapped here, farming, fishing and foraging amid the forest and extending networks of migration, trade and cultural exchange as far as the Orinoco Basin, the Gran Chaco forest and the Andes.

“The cultural diversity here is one of the greatest in the Amazon,” added Zuse. “There are materials dating back 9,000 years.”

The excavation was spurred by the construction of the nearby Santo Antônio hydroelectric dam. Such projects currently require archaeological surveys beforehand , but even this chance to rescue some priceless evidence is set to be foreclosed. Bolsonaro’s administration has revived proposals that prior surveys are only carried out where archaeological material is already proven to exist.

Most describe this as absurd: in most cases the archaeology is completely unknown until surveyed. “If they change the law, archaeology in Brazil is over,” said Bespalez.

The archaeologist Márjorie Lima at the dig in Tauary. Photograph: Adriano Gambarini

The vast data produced by such surveys has enabled archaeologists to challenge traditional ideas about the Amazon’s peoples – that they were primitive and constrained by the forest, rather than adapting to and shaping it – and redraw the shape of human history.

“Agriculture is older here in the Amazon than in the Andes,” said Bespalez.

Scientific expeditions have so far concentrated on accessible areas along major rivers. Forays into far western and inland areas could uncover untold additional evidence, further supporting estimates of a pre-Columbian Amazonian population larger than 10 million people.

But these investigations may now be put on hold indefinitely. In March, Bolsonaro’s administration announced a surprise budget cut of 42% to the science ministry and of 30% to university funding.

In September, the government indicated that CNPq, the main grant-providing body for trainee scientists will lose 87% of its research budget in 2020, while another scientific funding agency, Capes, will suffer cuts of 50%.

These drastic cutbacks could produce a “lost generation” among Brazilian scientists, forcing many archaeology departments to close, warned Jennifer Watling, an archaeologist at USP.

The cuts are defended by Bolsonaro’s government as balancing the books and encouraging researchers to collaborate with the private sector. But Lima argued that the president wants to “discredit the role of science”, because recent research poses a direct challenge to his vision of the Amazon as an untouched wilderness ripe for modern development.

Nine pre-Columbian urns containing human remains found by archaeologists of the Mamirauá Institute in Tauary. Photograph: Mamirauá Institute

Palaeobotanists have identified at least 83 species of plant in the Amazon – including manioc, cacao, sweet potato, peppers, fruits, palms and tobacco – that were domesticated and up to 5,000 that were exploited by pre-Columbian peoples across their houses, gardens, fields and orchards.

Even after European diseases killed many of its indigenous peoples from the early 16th century, the Amazon remained profoundly shaped by ancient human hands. And their descendants retain a strong understanding of how to manage their surroundings sustainably.

This knowledge is still evident in Tauary, where on a 20-minute walk through the forest resident Francisco Dias pointed out a dozen different trees whose bark, fruit, wood, sap and roots are used in food, medicine, ceramics, perfumes, adhesives and even to immobilise fish for the net.

Most researchers identify the violent, mass displacement of traditional communities likely to result from Bolsonaro’s policies as the biggest threat to their work – and a tragedy in itself.

Ash Asháninka: ‘If they want to conserve the planet, leave forested land to indigenous peoples.’ Photograph: -

“Large dams or mining will destroy a lot of archaeological sites,” said Anne Rapp Py-Daniel, an archaeology professor at Ufopa, a university in Santarém. “But seeing people losing everything worries me more.”

Neves argued that archaeologists can bring “another perspective” to the debate over the Amazon, polarised between conservationists emphasising its supposedly pristine state and those seeking to extract its undeveloped resources.

“The Amazon has to be protected, not only because it’s natural, but because it represents very sophisticated systems of knowledge that have been developed over the millennia,” he argued. “We don’t have any idea what we can learn.”

Leaders of an indigenous occupation in Rio de Janeiro known as the Aldeia Maracanã, who hope to set up a university to preserve and share such knowledge, agreed.

“International organisations should take note,” said Ash Asháninka, a member of a the Asháninka indigenous group in Acre state.

“If they want to conserve the planet, leave forested land to indigenous peoples. Because we know how to protect it and live there without destroying, poisoning or burning it. We know how to live well.”