Even here, Tuesday is an unusual day to die. At the weekend there is no shortage of bloodletting in this corner of the Amazon. Bar brawls, knife fights, lovers' tiffs, alcohol-soaked arguments, all with the same predictable coda: a slit throat, a shot to the head, a visit from Maraba's over-worked head of forensic science, José Augusto Andrade, and a gory crime-scene photograph splashed across the pages of a tabloid.

Tuesdays, though, are normally quiet. But 24 May this year was an exception.

The call came at about 10.30am, and Andrade was soon racing out of town towards the Praia Alta Piranheira settlement, a rural area about 55 miles from his antiseptic-scented morgue.

At the crime scene two bodies lay beside an earth track. Dozens of people crowded around the victims, who were instantly, predictably, recognisable. They were the rainforest activist José Cláudio Ribeiro da Silva, who had foretold his own death six months earlier at an environmental conference in the Amazon, and his wife, Maria do Espírito Santo.

If Tuesday was an unusual day for a double homicide, what Andrade saw was stranger still: Da Silva's ear had been hacked off, perhaps a trophy taken by the killers as proof their mission had been accomplished. "I'm used to barbarous crimes but not to seeing someone commit a murder, then mutilate a person," Andrade said. "It is not common."

Da Silva, also known as Ze Cláudio, and Espírito Santo were the latest in a string of environmentalists to die for their cause in the Brazilian Amazon. After nearly 15 years of campaigning against illegal loggers, as well as charcoal producers and cattle ranchers, they were gunned down not far from their jungle home on the settlement.

"They were moments that I would give everything to never have gone through," said Espírito Santo's sister, Laisa Santos Sampaio, a primary school teacher who lived on the settlement alongside the murdered couple.

Tears streaming down her cheeks, she repeated her roadside farewell. "I just remember asking: 'My sister, why have you left me?' I didn't know what to do."

In recent years the Brazilian government has made significant progress in slowing the destruction of the world's largest tropical rainforest, reducing the area of forest lost, from 10,500 square miles in 2004 to just 2,300 square miles last year. But a spate of brutal killings have underscored an uncomfortable truth: the authorities can stop the felling of the trees to some extent, but not the cutting down of environmentalists.

"This is the reality of this country," said Da Silva's youngest sister, Claudelice Silva dos Santos. "There is so much good stuff in Brazil. The Amazon is so beautiful. It has to be preserved. But this is what happens to those who try to protect it."

The murders of Da Silva and Espírito Santo were the highest profile environmental killings in Brazil since the murder of Dorothy Stang, 73. The American-born nun, who worked for the Catholic church's pastoral land commission, was shot in 2005 by two gunmen on a rainforest track in Para state. Among five defendants in the case was a wealthy rancher, Regivaldo Galvão, whose conviction for orchestrating her murder was upheld this month.

Few people believe such deaths will be the last. Many parts of the Brazilian Amazon remain off-limits to environmentalists, while government environmental officials go to certain regions only if escorted by rifle-toting police and helicopter back-up.

"The difference between here and the place where [Da Silva] and Maria were murdered is that this place is more isolated and you don't find rainforest defenders," said Marco Vidal, an environmental officer who had known the couple and was deployed in the region days after their execution.

With an assault-rifle slung around his shoulder, Vidal toured an illegal sawmill recently closed down by his forces. It was in a region known as Middle Land, one of the latest frontlines in the government's battle against deforestation, near the cattle-ranching frontier town of Sao Felix do Xingu.

"The rainforest defenders here were either killed or never made it this far due to the very real threat of being killed," he explained. "If NGOs such as Greenpeace tried to come here they would definitely be eliminated."

Da Silva and Espírito Santo had lived on the Praia Alta Piranheira settlement, on the banks of the Tocantins, in the Amazon state of Para. Founded in 1997 as part of a government land reform initiative, the 22,000-hectare (54,000-acre) settlement was split into plots, which were distributed to poor, landless Brazilians. The idea was that settlers would make a sustainable living from the forest, harvesting fruits and nuts.

It did not work out that way. When the settlement was created, about 85% of its land was pristine rainforest. The area has since been eaten away, its forests hacked down to produce charcoal for the region's pig-iron industry or transformed into huge cattle ranches. Facing financial hardship, many settlers were forced to sell their land or forests to the loggers and charcoal producers.

But Da Silva and Espírito Santo championed sustainability and railed against those people seeking to profit from the forest's destruction. The consequence was persistent death threats.

In a 2004 letter to Brazil's environment minister at the time, the rainforest defender Marina Silva, Espírito Santo issued one of many desperate cries for help. "We would like to inform you that we are being threatened with death because we do not agree with what is happening," she wrote. "Nature's enemies are working night and day."

Espírito Santo had described her two‑page letter as "an SOS", saying: "All we can now do is ask that you help us carry out our mission of preserving the forest … greed and capitalism have always been blind."

The frequent death threats were also registered with José Batista Gonçalves Afonso, a human rights lawyer and friend, who believes the government could and should have done more to protect the couple. "They were abandoned," he said. "They were exposed. And unfortunately they became easy targets for the gunmen of those who were interested in eliminating them."

Over the past 20 years Afonso has seen buried dozens of friends and colleagues – Amazon activists who stood up for the rainforest or the poor.

Nearly four months after Da Silva and Espírito Santo were murdered, police arrested three men in connection with the killings, in a dawn raid on a jungle camp about 32 miles from the Amazon town of Novo Repartimento. One of the men, José Rodrigues Moreira, a small-time cattle rancher, was accused of ordering the murders.

Family members suspect a wider conspiracy. Fearing for their lives, they have not returned to their homes on the settlement. "This is just the tip of the iceberg. There's much more going on here," said Claudelice, after police named their three prime suspects.

Sitting next to her on a sofa in the family's sitting room, Da Silva's elderly mother, Raimunda, said: "I feel like I have been abandoned in the middle of the world. My son meant everything to me. I love all of my children but he was my firstborn." With bloodshot eyes, she wept.

• The Crying Forest, an al-Jazeera documentary produced and directed by Tom Phillips and reported by Gabriel Elizondo, will be shown on Al-Jazeera English, starting on 29 September at 8pm and posted in full online at aljazeera.net/english