The Flamengo first team train at two other facilities, and the club are now preparing for a clash with Fluminese on Saturday night, February 9.
There is still no official information about what caused the fire.
The ages and identities of those killed were not released but the three injured were 14, 15 and 16 years old, the fire official said.
According to the fire department of Rio de Janeiro, there is one person in a serious condition among the wounded.
Brazilian clubs commonly host young players in dormitories while they are training with youth teams or at the club for trials, especially those from poor backgrounds or from outside the city.
"While Rio police sometimes kill people in legitimate self-defense, research from Human Rights Watch and other groups shows that many killings are, in reality, extrajudicial executions", the report said.
Flamengo are one of Brazil's biggest and most popular clubs, playing their home matches in Rio de Janeiro. Many players stay at the facilities while training.
"I am very happy".
The dream of many youths in Latin America's largest nation, victor of five World Cup titles, is to make it into the ranks of professional soccer. "I just spoke to Caix Suarez and he is alive", said Rodrigues, adding that the youth told him he ran when he saw the flames.
Passion for soccer runs deep in Brazil, and as news of the tragedy spread, numerous world's best players and top officials expressed condolences. "He lost his phone, and all of his things, but the important thing is he is alive".
"Just by thinking about the days and nights I spent in the training center gives me goose bumps", said the 18-year-old.
Players were reportedly sleeping in their dormitory when the fire broke out.
The main team had been due to practice at the same facility later in the morning. "Today I woke up and heard this bad news".
Flamengo is arguably Brazil's most famous club, with an estimated 40 million fans nationwide.
Six of the people who died are teenagers aged between 14 and 17 years old.
However, numerous lodgings have a reputation for poor health and hygiene standards.
Teenage Real Madrid forward Vinicius Junior, who came up through the youth ranks at Flamengo before signing with the European Champions in 2017 for 45 million euros ($51 million), posted a message on Twitter asking people to pray for the victims.