An environmental campaigner is killed every week in Brazil. Jonathan Watts and Karina Vieira travel to Lábrea in the heart of the Amazon to meet the people risking their lives

No one could accuse Nilcilene Miguel de Lima of being easily afraid. When loggers beat her and burned down her home in Lábrea – in the heart of the Brazilian Amazon – the environmental activist refused to give up her struggle. When they killed her dog and frightened away the armed guards who had been sent to protect her, she carried on without them. But after they murdered her fellow campaigners and warned her she would be next, the mother of four finally fled.

Today, she is in hiding hundreds of miles from home, looking out of the bars on the window of a temporary refuge in Manaus and wondering what happened to Brazilian justice and the world's interest in protecting the planet's greatest rainforest. "I'll be hiding for the rest of my life. The people who killed my friends and destroyed nature should be the ones in prison, but I'm the one who has no liberty," she says. "All I ever did was protect the families who tried to conserve the environment."

That is an increasingly dangerous ambition in Brazil where, according to a recent report by Global Witness, more environmental and land-rights campaigners have been killed than the rest of the world put together. The study found that, on average, one activist has been killed in the country every week since 2002. If that trend continues, four will die during the course of this World Cup, though very few cases are likely to make headlines.

Most of the murders occur in remote regions of the Amazon – places like de Lima's home of Lábrea in Amazonas state, where loggers, ranchers and land-grabbers are seizing property from smallholders, subsistence communities and indigenous tribes. Guns and muscle make the rules. Police are usually either absent, complicit or too weak to deal with the gangs of armed grileiros. The ethical consequences are immense.

Located in an arc of deforestation that stretches from Mato Grosso, through Acre and Rondônia across the Bolivian border, Lábrea is among the most remote, dangerous and important frontlines of environmental protection on the planet. Whether fighting climate change or conserving biodiversity, there are few more pressing struggles in the world than the one taking place here. Yet it rarely gets much attention in Brazil, let alone the rest of the world. The stage is too distant, the drama plays out too slowly and the economic interests are weighed against the activists, who are often accused by their enemies of holding back development.

Amazonian activist Nilcilene Miguel de Lima staring out of the window of a refuge in Manaus, Brazil, where she has been in hiding since her friends were murdered and she received death threats. Photograph: Jonathan Watts for the Observer

Getting to the flash points is a challenge. Most occur deep in the forest. The terminal at the nearest local airport is little more than a shed and it receives only seven scheduled flights a week. The road network is even less developed. Lábrea is at the end of the Trans-Amazonian Highway – a 4,000km road that was supposed to stretch from the east coast all the way to Peru, before the project ran out of funds and became mired in the mosquito and disease-infested swamps around the town.

As the town at the end of this line, Lábrea is a surprisingly bustling, sometimes surreal place with a population of more than 40,000 people – an indication of just how much human pressure is growing in the Amazon. A 20m statue of Mary with a neon halo dominates the central plaza along with dozens of brightly coloured – and almost completely unused – recycling bins placed every 10 metres along the path. A short walk down to the Purus river is a slum of boat-dwellers living on fetid waters; vultures perch on their corrugated tin roofs.

From here it is still three days' journey by motorboat to de Lima's home in south Lábrea. She is president of Deus Proverà, an association of Brazilian nut farmers and rubber tappers in the community of Gedeão in the south of Lábrea. Located several days canoe ride from the town, the area is dominated by a gang of gunmen who work for loggers and farmers. It is a hotspot for murder and intimidation. According to the Comissão Pastoral da Terra (Brazilian Pastoral Land Commission), six community leaders were assassinated in the Lábrea area between 2008 and 2013 and 51 local activists continue to receive death threats. Precedent suggests one in 10 of them will be murdered in the coming years.

De Lima is tougher than most. Struggle and tragedy have defined her life. She grew up in Xapuri in Acre, the headquarters of Brazil's most celebrated campaigner Chico Mendes, who was murdered in 1988 after he tried to halt loggers and establish extractive reserves for small farmers. These were areas where the right to harvest natural resources were granted to subsistence farmers, fishermen, rubber-tappers or nut harvesters, normally as buffers against the big farms and ranches that are responsible for the worst deforestation. De Lima's father was a co-founder of the Union of Rubber Tappers alongside Marina Silva, who later became the country's most effective environment minister. Her husband was killed, de Lima says, on the orders of loggers and half a dozen fellow community leaders have been shot, stabbed or beaten to death in arguments over land and conservation.

Among the most recent victims were Adelino Ramos, who was gunned down during a trip to Porto Velho after he exposed illegal loggers; Raimundo Nonato Chalub, who was killed on his farm after he denounced illegal deforestation and land seizures, and Dinhana Nink who was murdered in front of her six-year-old son after she vowed to name the gunmen threatening local smallholders. Nobody was charged in any of the cases.

Amazon deforestation Photograph: Leoffreitas/Getty Images/Flickr RF

The battle in Gedeão is now lost. The 160 families de Lima worked with have been driven out by the loggers and farmers, who have cleared 300 hectares of land. Now the same thing is happening in the neighbouring area of Riozinho. "They removed the people and now they'll remove the trees," she says. The residents are given little choice. "Gunmen come in the middle of the night and force people to sign documents saying they received compensation in return for leaving their land. In reality, they get nothing."

For her, the cost of speaking out has been attacks and abuse. A few years ago a lumber mill owner known as "Pitbul" reportedly took out a 100,000 reais (£27,000) contract on her head. The central government deployed nine força naçional guards to protect her, but after coming under fire they, too, were afraid to remain in Gedeão.

"There is no justice in Brazil. My house has been burned. I have been beaten. My family has been threatened. My friends have been raped and killed by loggers. Yet no one has been punished. I've begged for justice, but there is no justice in Brazil. We've all been abandoned by the state."

This reflects a global trend, according to Global Witness. Of the 908 killings worldwide it identified, fewer than 10% of cases were taken to court and just 1% resulted in convictions. The NGO said the murder rate is rising with three times as many victims in 2012 as in 2002 – a sign, it says, of the intensifying battle for scarce resources.

"Never has it been more important to protect the global environment and never has it been more deadly," writes Global Witness. But the campaigning NGO says the risks are rarely seen in their international context. "The problem is poorly understood. Where cases are recognised or recorded, they are generally seen in isolation and not as part of larger trend."

The scale of the problem is contentious. In the Global Witness report, the 448 deaths in Brazil since 2002 are more than four times more than the next most deadly country – Honduras, with 109. As the group acknowledges, this wide discrepancy is partly because Brazil has a strong civil society that can monitor and report on killings. In less open countries, countless cases go unreported.

There are also differences in the definition of environmental activism. In Brazil, most of the victims were not trying solely to conserve a pristine forest. Instead they want to exploit the natural resources themselves – albeit on a more sustainable scale than the big farms. This puts them up against powerful forces. Brazil has one of the most concentrated levels of land ownership in the world.

The agricultural lobby – or Banca Ruralista – says activists and smallholders are holding back development. Its voice has become increasingly influential as cash crops have grown more important to the Brazilian economy. The group's leader, Kátia Abreu, claims her bloc is likely to be a decisive force in the upcoming presidential election.

Against such influential interests, Lábrea activists feel isolated. "What we have here is more or less a Wild West. The government doesn't care about us. Even when there are laws, we are the ones who have to enforce them otherwise nobody respects them. We have to fight," says Wanderleide de Souza, the director of the National Council of Extractive Populations.

When we meet, she is recovering from her third bout of malaria this year and apologises for "looking yellow". For most of the past few years, however, disease has been a relatively minor concern.

De Souza has had countless phone calls warning her that she will be raped and murdered unless she gives up her work. One state deputy came to her home to intimidate her and called her a whore. "He thought that I would be the weakest link because I'm a woman, but the opposite is true. We have to be extra tough," she says.

Her determination and optimism are shared by others in northern Lábrea, where small-scale farmers and fisherman have benefited from the creation in 2008 of extractive reserves along the Purus and Ituxi rivers. These were established as buffers against the large-scale logging and farming operations that have destroyed swathes of the Amazon. But it puts the residents up against business interests and local politicians who are doing everything in their power to undermine the reserves and frighten off the residents.

Antônio Vasconcelos, a pastor and environmentalist, was a key figure in the creation of the reserves and has long been a target of opponents led by the former mayor of Lábrea, Gean Campos Barros.

"I'm terrified. I feel my life is in danger. I feel completely insecure," he says. "Whenever I hear someone approaching, I fear it could be someone coming for me."

Several years ago, his name was found on a hit-list of community activists. When two of the others on the list – Zé Cláudio and Adelino Ramos – were murdered, the government provided round-the-clock protection. For three years, Vasconcelos lived with 13 police officers. "It didn't stop the threats," he says. "Every night someone would call to say they had a bullet not only for me, but for each of my guards."

Such fears have not stopped him campaigning against illegal loggers, farmers and plans for hydroelectric dams. Vasconcelos says he was inspired by Chico Mendes. "He told us we must fight for what we believe and not be intimidated. He created many Chico Mendes in Lábrea and elsewhere," he says. "I consider myself the second Chico Mendes. I am doing all I can to protect the environment in the Amazon, but sometimes I wonder if it is worthwhile because the government doesn't protect us."

There are similar stories of intimidation, threats and resistance from other activists in Lábrea. Francisco Monteiro Duarte, the president of Apadrit, which covers the 776,000 hectare Ituxi reserve, is recovering from a beating by his brother – carried out, he says, on the orders of local businessmen. Concerned that the next attack could be deadly, his family have begged him to quit. He understands why. "I'm in fear of my life because so many people like me have been killed. I've lost count of the number who have died since Chico Mendes," he says.

Duarte's greatest fear is an ambush during the four-hour canoe journey through the dark swamps and narrow channels from Lábrea to his home in the reserve. We navigate similar waters on the way to a conservation workshop with José Maria Ferreira, one of a new generation of activists.

Young and charismatic, Ferreira is the first person from an extractive community to head a regional office of the government's main conservation body, the Instituto Chico Mendes de Conservação da Biodiversidade. He has helped the small river communities in the Ituxi reserve to profit from environmental protection. Five hundred people in the community now receive a bolsa verde (green stipend) and money goes into the area for conserving pirarucu – the largest freshwater fish in South America – that is starting to recover thanks to a new management system. But this means confronting illegal fisherman, something Ferreira urges the local community to do during a talk at a school which sits on stilts above the muddy river bank. Several residents complain the rewards are too small and the dangers too great. Ferreira knows the risks all too well. His institute was temporarily ejected from Lábrea in 2010 after the former mayor stirred up a mob against them.

"I'm in the crosshairs. The politicians in Lábrea want to get rid of me because I'm stopping them from making money," he tells the participants. "I feel very threatened but it doesn't weaken me and the fight for conservation. Threats are part of the job. Once, my wife was beaten up and the attackers told her, 'Next time, we kill your husband.' Last year they broke into my home, held a knife against the neck of my one-year-old child and ordered my wife to tell them where I was."

A local woman implores him to be careful. "Yesterday someone stopped me and told me to tell you that you are going to lose your head," she says. "God bless you for the work that you do. I should take a picture of you so I can remember what you look like."

After we return to the river and navigate away from the community, Ferreira says he will not be scared off. "I have always loved what I am doing and now we are getting some good results so I feel we are really going in the right direction."

His story – like that of so many other activists that we met – is simultaneously uplifting, depressing and worrying. The residents of the extractive reserves receive some support from some sectors of the government – the Human Rights Secretary and the Environment Ministry – but the powerful agribusiness lobby is increasingly influential. The rights of extractive populations seem a low priority for the president, Dilma Rousseff, conservation even less so. Damningly, after almost a decade of slowing deforestation, land clearance spiked back up by 28% last year.

That should make anyone concerned about ethics think twice before buying soy, beef, nuts, furniture, timber or other products from Brazil unless they are certified as being from a supplier that works with extractive communities or sustainable farms. It should also encourage more support for the campaign for a UN Human Rights Council resolution to address the heightened threat posed to environmental and land defenders around the globe.

Activists such as de Lima, Ferreira, Duarte, Vasconcelos and de Souza face very serious dangers. But despite the killings and threats, Brazil's extractive communities are alive and kicking. The least they deserve is the outside world's support.