Phillips, 57, and Pereira, 41, had been missing since 5 June after they were last seen in a remote part of the Amazon rainforest in the Javari Valley, the second-largest Indigenous territory plagued with violent crimes by illegal poachers, drug traffickers and illegal miners.
The suspect led the officers deep into the forest where human remains were buried, seemingly ending more than a week-long search for the missing pair.
Officer Eduardo Alexandre Fontes said the 41-year-old suspect, identified as Amarildo da Costa de Oliveira and nicknamed Pelado, used a firearm to kill Phillips and Pereira.
However, the suspect’s family has accused the police of torturing him into a confession, while denying that he was involved in any wrongdoing.
Search teams brought body bags to the docks at the city of Atalaia do Norte. Officials said they would conduct an autopsy to confirm whether the remains are of the pair.
“We would have no way of getting to that spot quickly without the confession,” the investigator said of the place where police recovered human remains.
“We found the bodies three kilometres into the woods,” he said, adding that rescue teams had to travel for nearly an hour and 40 minutes on the river and 25 more into the woods to reach the burial spot.
On Monday, items belonging to both missing men – including their clothing and Phillips’s health identification card – were found, according to police.
The mortal remains of the pair will be returned to families within days following a confirmation, police said.
Amazonas state police officer Guilherme Torres noted that the missing men’s boat had not been found yet but police knew the area where it was allegedly hidden. Officers added that the engine of the boat was removed.
“They put bags of dirt on the boat so it would sink,” Mr Torres.
Phillips’s wife, Alessandra Sampaio, in a statement, said the tragic outcome “puts an end to the anguish of not knowing Dom and Bruno’s whereabouts”.
“Today, we also begin our quest for justice. I hope that the investigations exhaust all possibilities and bring definitive answers on all relevant details as soon as possible,” she said.
“Now we can bring them home and say goodbye with love.”
She thanked everyone involved in the search operation, especially the “Indigenous peoples and Univaja [an association of Indigenous peoples of the Javari Valley]”.
Indigenous leaders who sounded the alarm over their disappearance and began the searches deep into the forest were reportedly not invited to Wednesday’s press conference in Manaus.
The two men’s deaths are linked to illegal fishing, as Pereira was reportedly threatened by people engaged in the contraband activity before going missing. The father of three, who previously led the local bureau of the federal Indigenous agency known as Funai, took part in several operations against illegal fishing.
Pereira was fired from his position at Funai in what was seen to be a politically motivated move, soon after president Jair Bolsonaro came to power in the country.
Meanwhile, British prime minister Boris Johnson said he was “deeply concerned” about the disappearance of Phillips and was working with Brazilian authorities to investigate the case.
“Like everybody in this House [of Commons], we’re deeply concerned about what may have happened to him. FCDO [Foreign Office] officials are working closely now with the Brazilian authorities,” Mr Johnson told lawmakers.
Phillips has written for The Guardian, The Financial Times and other publications and was travelling in Brazil for work purposes with Pereira when they went missing.
(Additional inputs from agencies)