Firefighters said they arrived at the Ninho do Urubu, a state-of-the-art training center that was expanded and opened only two months ago, shortly after 5 a.m. (0700 GMT) to find the building engulfed in flames. February 8, in an accommodation block at the facility of the club.
The fire reportedly broke out as players were sleeping. A gun battle followed and at least 12 people died.
Local media reported that the fire started in a dormitory where youth players sleep.
Many players, particularly those who live outside of Rio de Janeiro, stay at the facilities while training.
The three injured youths - Jhonata Cruz Ventura (15 years), Cauan Emanuel Gomes Nunes (14), and Francisco Diogo Bento Alves (15) were taken to area hospitals, the club said on Friday.
"The air conditioner caught fire, and I ran out", said Felipe Cardoso, a player with the under-17 side.
Youth league teams also train at the facility, known as Ninho do Urubu, which means "the vulture's nest".
Rio de Janeiro is one of the world's most violent cities with frequent shootouts between police and drug gangs and an annual homicide rate of around 50 per 100,000 inhabitants. "Thank God I managed to run and I'm still alive".
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.
Flamengo is perhaps the most famous club in the country, with an estimated 40 million fans nationwide. "Lives are gone. May the Black and red nation have the strength and faith to overcome this moment".
Outside the complex, an AP reporter saw two ambulances and a fire truck enter.