Work is proceeding to determine the cause of death, police said in a statement.
The remains of a second person, believed to be that of indigenous expert Bruno Pereira, were still under analysis, a report by CNN Brasil said earlier on Friday.
Pereira and Phillips vanished on June 5 in the remote Javari Valley bordering Peru and Colombia. Earlier this week, police recovered human remains from a grave in the jungle where they were led by a fisherman, Amarildo da Costa Oliveira, who confessed to killing the two men.
Phillips, a freelance reporter who had written for the Guardian and the Washington Post, was doing research for a book on the trip with Pereira, a former head of isolated and recently contacted tribes at federal indigenous affairs agency Funai.
Police said their investigation suggested there were more individuals involved beyond Oliveira and that they were now looking for a man named Jeferson da Silva Lima.
He is the third suspect named by police after Oliveira and his brother, Oseney da Costa, who was taken into custody this week.
"There is an arrest warrant issued by the State Court of Atalaia do Norte against Jeferson da Silva Lima, aka 'Pelado da Dinha', who has not been located at this time," police said.
"The investigations indicate that the killers acted alone, with no bosses or criminal organization behind the crime."
Local indigenous group Univaja, however, which played a leading role in the search, said: "The cruelty of the crime makes clear that Pereira and Phillips crossed paths with a powerful criminal organization that tried at all costs to cover its tracks during the investigation."
It said it had informed the federal police numerous times since late 2021 that there was an organized crime group operating in the Javari Valley.
INA, a union representing workers at Funai, shared that view.
"We all know that violence in the Javari Valley is linked to a wide chain of organized crime," it said in a separate statement.
Police said they were still searching for the boat Phillips and Pereira were traveling in when they were last seen alive.
U.S. State Department spokesman Ned Price on Friday called for "accountability and justice," saying that Phillips and Pereira were murdered for supporting conservation of the rainforest and native peoples.
"Our condolences to the families of Dom Phillips and Bruno Pereira... We must collectively strengthen efforts to protect environmental defenders and journalists," Price said on Twitter.