AFL deputy chief executive Gillon McLachlan said the investigations into the potential breaches would likely take months rather than weeks, meaning any sanctions would not be in place before the season begins on March 22.
The Australian Crime Commission (ACC) report only identified two specific cases where illegal performance enhancing drugs may have been used in the AFL.
McLachlan confirmed the club being investigated for potential multiple breaches was Essendon - who went to the AFL with concerns over supplement use before the ACC handed down their report on Thursday.
"I think it's reasonable to say, given that the Essendon football club has come forward to the AFL and to ASADA, and proactively advised us of concerns they have, it's reasonable to talk to that," said McLachlan.
"The AFL is aware of potential multiple breaches at that club."
McLachlan refused to reveal the identity of the individual player under investigation or the club he plays for.
"The AFL is aware of one case involving the possibility of WADA prohibited performance enhancing drug use by one player at one club," said McLachlan.
"The AFL is aware that a second case involves the possibility of WADA prohibited performance enhancing drug use by multiple players at one club.
"In this case it's possible that players were administered the WADA prohibited substances without their knowledge or consent."
McLachlan said the AFL was also aware of other cases involving illicit drug use.
But the league had not been warned of any specific instances of suspected match fixing in AFL competition.
The Bombers play the opening match of the home and away season against Adelaide at AAMI Stadium on March 22.
McLachlan said it was highly unlikely the investigations into alleged drug abuse at Essendon and by the other player would be completed by then.
"It's not going to be as quick as everyone would like," said McLachlan.
"The reality is that the investigators, which is ultimately ASADA in partnership with the AFL, have to get the right answers and that will take as long as it takes.
"It's more likely to be months rather than weeks."