Jeferson da Silva Lima was on the run, but surrendered to the police station of Atalaia do Norte, in the remote valley of Javari, on the border of Peru and Colombia.
“The inmate will be questioned and remanded to a custody hearing,” federal police said in a statement.
A forensic examination carried out on the human remains found in the area on Friday confirmed that they belonged to Phillips. The remains of a second person, believed to be indigenous expert Bruno Pereira, were still being investigated.
Phillips, a freelance reporter who had written for the Guardian and the Washington Post, was researching a book on the trip with Pereira, a former isolated tribes official and recently contacted the federal Indian affairs agency Funai.
They disappeared on June 5 while traveling alone in the region by boat.
Police have so far arrested Amarildo da Costa Oliveira, a fisherman who confessed to killing the two men, and his brother, Oseney da Costa, who was taken into custody earlier this week.
Federal police said on Friday the killers acted alone, a claim local indigenous group Univaja disputed, adding that it had repeatedly told authorities that an organized crime group was operating in the Javari Valley, an area which has attracted cocane smugglers, as well as illegal hunters and fishers.
Law enforcement sources told Reuters the investigation focused on people involved in illegal fishing and poaching on indigenous lands.