The suspect, 41-year-old Oseney da Costa de Oliveira, is a fisherman and the brother of the man who is so far considered by the police as the main suspect in the case, Amarildo da Costa de Oliveira, also 41 years old, nicknamed Pelado.
Federal police also said in a statement that they had seized ammunition and a paddle, but did not say why the items were confiscated, who they belonged to or where they were found.
De Oliveira told the Associated Press on Friday that he had visited Pelando in jail and was told that local police had tortured Pelando on his own boat, which was also seized by authorities.
Federal police did not immediately respond to a request from the AP asking why Oseney da Costa de Oliveira was named in the statement, which is not a formal procedure by force.
The natives who were with the expert Bruno Pereira and the British journalist Dom Phillips said that Pelando hit them with a rifle the day before the disappearance of the two men.
He has denied any wrongdoing and claims that police tortured him to try to get a confession, his family told the AP.
The search for the missing continued on Tuesday, following the discovery of a backpack, laptop and other personal items that sank in a river on Sunday.
Pereira, 41, and Phillips, 57, were last seen June 5 near the entrance to the Xavari Valley Indigenous Territory, which borders Peru and Colombia.
Federal police issued a statement Monday denying media reports that the bodies of the two men had been found.
Investigators are concentrating their efforts around a spot on the Itaquai River near the town of Atalaia do Norte, where volunteers from the Native Matis group said Saturday they found a tarpaulin from the boat used by the missing.
The Javari Valley has seven well-known Indigenous groups – some of which have only recently come into contact, such as the Matis.  The valley also has at least 11 contactless groups, making the area the largest concentration of isolated tribes in the world.
Violent clashes broke out in this area between fishermen, poachers and government officials.  Violence has escalated as drug gangs fight for control of waterways for cocaine transport, although the Itaquai River is not a known drug trafficking route.