An investigators report obtained by The Associated Press on Tuesday shows Eduardo Bandeira de Mello and seven others were charged over the fire at the club's training facility.
Mello did not respond to a request for comment. The Rio de Janeiro-based team said it did not know of the charges.
The report signed by investigator Marcio Petra says Mello and a monitor "could and should have acted to avoid the result, which, by omission, transforms them into the perpetrators" of the fire.
Officials have not given an official cause for the blaze, but said they investigated the possibility an air conditioning unit caught fire after a power surge.
Flamengo's academy players, between the ages of 14 and 16 and identified as potential future professionals, were sleeping in their quarters when the fire broke out.
Documents showed the area that burned had been licensed as a parking lot, not a dormitory. Since the dormitory's existence was not registered, firefighting officials said they had not inspected or certified it.