"The first detainee decided voluntarily at the end of the afternoon to confess to a crime, during the confession he gave details of where he buried the bodies (...) and where he hid the boat" in which the two men were traveling, the official explained at a press conference.
Amarildo da Costa Oliveira said he killed Phillips, 57, a contributor to the British newspaper The Guardian, and Pereira, 41, with bullets.
At the site indicated by the detainee, police found human remains that will be analyzed for identification, Da Costa said.
The remains were found 3.1 kilometers from where the personal belongings of the two men who disappeared days earlier were found.
A brother of Da Costa, Oseney da Costa de Oliveira, is also in custody, but he did not confess to participating in the crime.
The superintendent said that a third person identified by Amarildo da Costa Oliveira is under investigation.
Hours earlier, the Minister of Justice and Public Security, Anderson Torres, had reported the discovery of remains.
"I have just been informed by the Federal Police that 'human remains were found at the site where excavations were being carried out. They will be analyzed," the official said on Twitter.
Phillips and Pereira disappeared on June 5 in the Javari Valley region of northern Brazil, near the border with Peru, when they were on their way to visit an indigenous monitoring team so the journalist could do some interviews.
On Wednesday, the Brazilian president, Jair Bolsonaro, assured that Phillips was "frowned upon" in the area due to his reports, and that is why he should have been more careful.
"That Englishman was frowned upon in that region because he did many reports against "garimpeiro," environmental issues; in that region, quite isolated, there were many people who did not like him; he should have redoubled the attention with himself, and decided to make an excursion," he criticized in an interview on a YouTube channel, as reported by the portal G1.
Bolsonaro added that in the area where the two disappeared, there are "river pirates, everything you can imagine" and that it is "very reckless" to walk there without being properly prepared physically and armed with authorization from the National Indian Foundation (Funai).
Days before, the president had already indirectly blamed the missing people for their situation, saying that they were in the Amazon on an "adventure," discrediting the work of the British journalist, collaborator of "The Guardian."