Among the most famous to come through the club are Zico, a former No. 10 on Brazil's national team; top goal-scorer Adriano, who rose to fame at Inter Milan; and current Real Madrid star Vinicius, Jr., who not long ago was living in the structure destroyed by the fire.
The fire reportedly broke out as the players were sleeping, the cause of which is unknown.
According to the fire department of Rio de Janeiro, there is one person in a serious condition among the wounded. We only found bodies inside.
Because of those heavy rains the football facility remained without electricity or water on Friday as the fire broke out, G1 reported.
After years of financial difficulties, Flamengo last year spent 23 million reais ($6.2 million) to expand the Ninho do Urubu facilities.
Passion for football runs deep in Brazil, and as news of the tragedy spread, numerous world's best players and top officials expressed condolences.
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The Ninho do Urubu, or Vulture's Nest, is so called because the club's symbol is a vulture. It took around two hours for the fire to be brought under control. "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 in the morning.
Several of the club's best-known young talents trained there, including midfielder Lucas Paqueta, who made his debut for AC Milan in January, and Vinicius Junior, who joined Real Madrid previous year.
Police said agents were tipped that as many as 20 perpetrators were at a community municipal savings building in Rio de Janeiro.
Flamengo won the Copa Libertadores in 1981 and won the Intercontinental Cup in the same year, beating Liverpool 3-0 in the final in Tokyo.
"It's the worst tragedy in the club's 123 years", said Flamengo president Rodolfo Landim, who visited the scene. "Lives are gone. May the Black and red nation have the strength and faith to overcome this moment".
David Luiz, the Chelsea defender with 56 caps for Brazil, added on Instagram: "Deep sadness!"