Indigenous activists and lawyers in Brazil have voiced shock and dismay after the federal police chief leading the investigation into the murders of Bruno Pereira and Dom Phillips was unexpectedly removed from the case. Francisco Badenes, an experienced investigator, had been running the inquiry into the 2022 deaths of the Brazilian Indigenous expert and the British journalist since the second half of that year. Pereira and Phillips were ambushed and killed near the Amazon town of Atalaia do Norte while returning from a reporting trip to the entrance of one of Brazil’s largest Indigenous territories. Badenes was also responsible for investigating the 2019 murder of Maxciel Pereira dos Santos, an officer from the Indigenous protection agency Funai who had worked with Pereira and was killed in the nearby border city Tabatinga. Late last month, for reasons that remain unclear, the Brasília-based investigator was taken off both cases, as well as a third scrutinising a 2020 massacre allegedly perpetrated by military police officers in another part of the Amazon. Eliesio Marubo, a lawyer for Univaja, the Indigenous association where Pereira worked, said removing Badenes from those cases was “a big step backwards”. He feared it would hinder police investigations and efforts to combat the organised crime network suspected of committing those crimes and others. “This is prejudicial [to the inquiry] … There needs to be a public interest justification for changing him – and I don’t see any kind of public interest justification here,” said Marubo, who was Pereira’s friend. Thais Rego Monteiro, a lawyer who represents Santos’s family, said they were “dismayed, saddened and disheartened” by reports that Badenes – who has spent much of the last 30 years investigating murders and death squads – had been removed. Monteiro, who did not know the reasons for the change, called Badenes a diligent, skilful and efficient investigator who had made significant breakthroughs in the Santos case after years of inaction. “[Relatives] feel downcast and really troubled at this change,” Monteiro said, calling it “an impediment to the advance and the conclusion of this investigation”. The federal police declined to make an official comment on the changes. However, a federal police source confirmed a new investigator would take charge of the three inquiries and said they hoped the change would speed up the investigations into the murders of Phillips, Pereira and Santos. In a statement, Univaja voiced “deep concern” over the situation and said there was “intense suspicion” over the unexplained move. The group, which is based in Atalaia do Norte, has asked the justice ministry for an urgent clarification. Pereira and Phillips were killed while journeying along the Itaquaí River early on 5 June 2022. They had been visiting Indigenous patrol teams. These are trying to protect the Javari valley Indigenous territory, a vast expanse of rainforest reputedly containing the world’s largest concentration of isolated peoples. The alleged murderers – a trio of fishers called Amarildo da Costa de Oliveira, Oseney da Costa de Oliveira and Jeferson da Silva Lima (also known as Pelado da Dinha) – are being held in custody in high-security prisons and are expected to face trial next year. They are suspected of committing the crime on behalf of Ruben Dario da Silva Villar, whom police have accused of running a transnational illegal fishing network that preys on those protected Indigenous lands. Villar has also been arrested and charged. Amarildo da Costa de Oliveira and Jeferson da Silva Lima confessed to the murders in the days after Pereira and Phillips disappeared but later claimed they had acted in “self-defence” after being shot at by the Indigenous expert. Their co-accused have denied involvement in the crime. However, Indigenous activists suspect an even bigger conspiracy could lie behind the killings of Phillips, Pereira and Santos and say criminal groups continue to operate in the remote region where they were murdered. Marubo, who hoped Badenes would be reinstated, said he feared replacing the investigator would hamper efforts to catch the criminals responsible for the murders and for illegal poaching, drug trafficking and mining in the Javari. “This will really make the investigation take a different course to the course that we believe will lead to the true culprits – not just for the murders of Bruno and Dom, but Maxciel too,” he said.