AFL deputy CEO Gillon McLachlan said at a hastily-arranged media conference on Sunday that Essendon was being investigated over alleged multiple cases of use of World Anti-Doping Agency-banned performance-enhancing drugs by players, possibly "without their knowledge or consent".
He declined to name the club or player involved in the other investigation.
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McLachlan said the AFL wasn't aware of any ongoing performance-enhancing drug use among AFL players.
While the scope of the AFL's immediate concerns is now clearer, McLachlan declined to go into specifics when it comes to illicit drugs.
"No, I'm not going to be able to put a number on it," he said.
"The use of illicit substances in our code is a problem."
McLachlan said he was seeking to publicly clarify the AFL's position because "at the moment every player in every club is potentially a drug cheat.
"I am not in anyway downplaying the vulnerabilities and the risks outlined last Thursday.
"What we know right now is the two instances of potential performance-enhancing drug use, no potential issues around match fixing (and) some vulnerabilities in use of illicit substances. That's what we know."
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Earlier on Sunday, Home Affairs Minister Jason Clare confirmed negotiations were under way with the Australian Crime Commission, the AFL and NRL to ensure clubs were aware of allegations levelled against them or their players.
He said the clubs would then have the opportunity to publically confirm they were under investigation.
"We've given the names of the clubs to both the NRL and the AFL. The NRL and the AFL have asked for permission to tell the clubs that are affected by the investigation," Mr Clare told ABC TV's Insiders on Sunday morning.
"The crime commission agrees and we're taking action to allow both the NRL and the AFL to tell the clubs that are involved in this investigation.
"Then it'll be up to the clubs to put their hand up and say 'Yes, we are one of the clubs affected by this investigation'," he said.
This latest development signals a desire from authorities to protect the innocent.
"The veil of suspicion is hanging over all clubs. The more information we can get out there the better. Silence is not going to be the solution here," Mr Clare said.
He also confirmed some athletes had come forward of their own accord since the release of the report.
Meanwhile Geelong has issued an open letter to supporters, saying it welcomed investigations by the AFL and the Australian Sports Anti-Doping Agency and it had "nothing to hide".
"Our club has been drawn into the public discussion because one of our past employees is being mentioned and this is prompting questions about how we have conducted ourselves in recent years," the letter from president Colin Carter and CEO Brian Cook said.
"Let me assure you that we have nothing to hide. Our processes are robust and we are confident that they stand up to any examination.
"However, we know that this will not be enough for some people who will doubt the legitimacy of the game and are disillusioned. And so, we believe it is important that the story of a club that did everything 'by the book' and achieved great success through hard work, professionalism, team work, unity and commitment should be celebrated. We owe that to everyone who has contributed."
Carter and Cook said club doctors "directly determine all treatments and the use of all supplements by our players. We believe our protocols are best practice and that is why we are confident in our position."
