Gordon acknowledged the toll that the AFL and the Australian Sports Anti-Doping Authority's investigation must have taken on former Bombers' chairman David Evans and said the saga was an "unprecedented" issue for the AFL.
Evans stood down on Saturday night after the stress of the past five months caused a rapid decline in his health.
He also said Ziggy Switkowski's description of Essendon's football department as a "pharmacologically experimental environment" during 2012 had sharpened his own focus on ensuring the Bulldog players were protected from such treatment.
"I think those words will resonate; I know they have with me and across the industry in terms of this whole issue," Gordon told radio station 3AW on Sunday.
"If some good comes out of it, it's the increased focus that every club and all of the football departments will have on what substances are around and the need to protect the footballers and have a solid regime."
Gordon was appointed as David Smorgon's successor in December for his second term at the helm of the club after a seven-year stint that ended in 1996.
He said the revelation of Essendon's situation and the subsequent investigation by the AFL and the Australian Sports Anti-Doping Authority in February prompted a thorough review of the club's medical processes.
"I certainly did a very thorough reconnaissance in conjunction with [CEO] Simon Garlick to review it, speak to the director of medical services, speak to the doctors, do a very broad and deep cross-section of the club," he said.
"Thankfully, [we're in] a position to assure the community and our supporters there are no such issues at the club.
"The only injections or substances for Bulldog players are administered by doctors and they're therapeutic and they're well within the confines."
Fairfax Media published a story on Saturday alleging police may investigate whether Essendon players were deceived into taking part in a "secret drug trial".
Gordon said that report exacerbated what was already a worrying situation.
"I think what we saw on The Age front page yesterday highlights to me an extra issue which is, footy is a big industry these days and the principal concern for these people but it's not the only issue," he said.
"Giving young players substances of unknown effect in an experimental environment, in one sense, you really are playing with their futures and their lives.
"These are serious issues."
Gordon emphasised the voluntary nature of the position of chairman or president of a football club, and sympathised with both Evans and the recently departed Melbourne president, Don McLardy.
"When you reflect back on what David Evans would have gone through this year, to say the least it must have taken an extraordinary toll on him," he said.
"Guys like David and Don McLardy before him - I got to know too as a good guy - they do a lot for their clubs and sometimes the way it all pans out is quite unfair, isn't it?"
Jennifer Phelan is a reporter for AFL Media. Follow her on Twitter @AFL_JenPhelan
