A new investigation has linked the world’s biggest meat company JBS, and its rival Marfrig, to a farm whose owner is implicated in one of the most brutal Amazonian massacres in recent memory.

The report by Repórter Brasil comes as JBS faces growing pressure over transparency failings in its Amazon cattle supply chain.

On 19 April 2017, nine men were brutally murdered in what became known as the "Colniza massacre". The men had been squatting on remote forest land in the state of Mato Grosso when their bodies were found, according to court documents. Some showed signs of torture; some had been stabbed, others shot.

According to charges filed by state prosecutors in Mato Grosso, the massacre was carried out by a gang known as "the hooded ones". The aim, they said, was to terrify locals, take over land they lived on and extract valuable natural resources. The first reporter to reach the lawless, far-flung region only got there a week later.

On 15 May 2017, prosecutors said they had charged Valdelir João de Souza, a farmer who owned two timber companies on neighbouring land, and four others with homicide and forming or being part of an illegal paramilitary group. Prosecutors said de Souza had ordered the massacre, although he had not been present when it occurred.

Since then de Souza has been a fugitive. But in April 2018 two adjacent areas of land – Três Lagoas and Piracama farms - in nearby Rondônia state were registered under his name (one of the oddities of the Brazilian property system is that landowners register their own land and boundaries). The two farms covered 1,052 hectares (2,599 acres) in an area set aside by the government for low-income agricultural workers. Satellite images show extensive deforestation on the Três Lagoas farm in 2015.

Government sanitary records seen by Repórter Brasil show that on 9 May 2018 143 cattle were sold by the Três Lagoas and Piracama farms to a farm owned by Maurício Narde.

Minutes later Narde’s farm sold 143 animals of the same sex and age – 80 female cattle between 13– 24 months old and 63 female cattle over 36 months old – to a JBS meatpacker.

In June 2017, according to court documents in a separate case, Narde worked at a sawmill owned by de Souza in Machadinho d’Oeste in Rondônia state. He still works at the same sawmill, although it has since changed its name and is no longer controlled by de Souza. Reached by telephone by the Guardian, Narde confirmed the transaction but did not explain why he had sold the cattle after buying them minutes beforehand.

"We buy and sell, just to keep things moving," he said, before deciding not to answer any more questions and concluding the interview.

The quick sale of the cattle suggests what environmentalists call "cattle laundering" – when cattle from a farm that has environmental issues sells cattle to a "clean" farm. This gets around monitoring systems because meat companies including JBS do not monitor these "indirect suppliers".

"This series of coincidences suggests a common practice, which is the triangulation of animals," said Mauro Armelin, director of Friends of the Earth Brazil. "It is a practice that could indicate cattle laundering."

On 25 June 2018, according to government sanitary records, Três Lagoas also sold 153 head of cattle to the Morro Alto farm in Monte Negro, Rondônia, owned by José Carlos de Albuquerque.

In the following months de Albuquerque sold dozens of head of cattle to JBS and Marfrig slaughterhouses.

De Albuquerque told Réporter Brasil that the sale had never been completed – but the report cited sanitary records showing the cattle had, in fact, entered the Morro Alto farm. Contacted by the Guardian by phone and email, he declined to answer questions.

The Repórter Brasil investigation highlights the difficulties that Brazil’s big meat companies have in monitoring their supply chains.

JBS and other big companies such as Marfrig committed to not buying from farms involved in illegal deforestation in two separate agreements signed with Greenpeace and Brazilian prosecutors in 2009 and subsequent years. Under the Greenpeace deal, the companies also promised to remove producers accused of land grabbing or convicted in rural conflicts from their suppliers lists. The deal with federal prosecutors similarly bans farms that have been convicted of involvement in rural conflicts, or that are being investigated.

Greenpeace quit their deal in 2017, after JBS was fined for buying cattle from farms in illegally-deforested areas in the Amazon state of Pará. An audit by federal prosecutors found that 19% of the cattle JBS purchased in the state in 2016 had "evidence of irregularities".

In the years following the cattle agreement, JBS made enormous progress in improving its monitoring of Amazon suppliers and the company defended its sustainability in a statement.

"We monitor over 280,000 square miles, an area larger than Germany, and assess more than 50,000 potential cattle-supplying farms every day, as well as conducting daily checks of all purchases to ensure compliance with strict standards. To date we have blocked more than 8,000 cattle-supplying farms due to noncompliance," it said.

But while the company now has a complex system in place to monitor its direct suppliers, it is still unable to monitor its indirect suppliers – those farmers who sell to farms that then sell on to JBS.

De Souza’s case has yet to be concluded. Ulisses Rabaneda, a lawyer representing de Souza, told the Guardian that he had decided not to reply to questions from the media at this stage in the court proceedings.

In an interview with the Gazeta Digital in 2019, de Souza said he was innocent of all charges, had never been involved in death squads, and remained a fugitive because he was scared he would be murdered by the real killers if he handed himself in.

"I never went around armed, so why at my age of 41, with solid companies, a peaceful life, no debts, without any problems, would I do something so barbaric?" de Souza said in the interview. "I built everything with the honesty and effort of my family. Why would I throw it all away?"

JBS told Réporter Brasil that de Souza was not a supplier and that it does not "acquire cattle from farms involved in deforestation of native forests, invasion of indigenous reserves of conservation, rural violence, land conflicts, or that used slave or child labour".

"JBS reiterates that any attempt to link the company to the person mentioned in the report, who was never on its list of suppliers, is irresponsible," the company told the Guardian.

Marfrig declined to comment on the investigation and sent the statement it had previously sent to the Guardian in December in which the company recognised that 53% of its Amazon cattle comes from indirect suppliers.

"Marfrig is fully aware of the challenges related to the livestock production chain and recognises its role as an important transformation agent to ensure production vis-à-vis the conservation of Brazilian biomes, especially the Amazon," the company said.

It detailed measures including a supplier monitoring platform and its Request for Information (RFI) tool, in which suppliers voluntarily list the farms they may have acquired animals from. The company says a third of the cattle it sources in the Amazon come with an RFI, and it is now working to improve the process with World Wildlife Fund.

In 2017, a Greenpeace report published after the Colniza massacre said a company owned by de Souza, called Madeireira Cedroarana, had accumulated around $150,000 (£116,000) in unpaid fines over a decade from Brazil’s environment agency, Ibama.

Between January 2016 and October 2017 the company exported thousands of cubic metres of timber to the US and Europe. In 2018 it changed its name to Colmar Madeiras; it continues at the same address, but de Souza is no longer its controlling partner. In the interview with Gazeta Digital, he said his company had challenged fines it had received.