And he described the targeting of players by anti-doping authorities as 'a witch-hunt'.
Madden said while sanctions for players were mandatory, administrators at AFL clubs potentially had too much "wriggle room" if players were found guilty of doping.
He said although mandatory penalties for players were fair, they should be tightened for club officials.
"The sanctions for players or sportspeople are mandatory - if it's in the system, it's in the system and the sanctions are locked in. Whereas for others, there's a fair degree of discretion," Madden said on SEN radio on Tuesday morning.
"I think what is unreasonable is if you're in the system at any other level of the hierarchy, you can escape mandatory sanctions.
"There's a fair degree of discretion about what may or may not be imposed on you and for what reason in these matters."
Madden said he was not referring to Essendon, the club at the heart of the Australia Sports Anti-Doping Authority investigation into its use of supplements last season, but to all clubs and sportspeople in general.
"At the end of the day the players are locked into sanctions and the worst part is that's where they earn their income," he said.
"Whereas other people at other levels within any hierarchy, they can potentially earn an income at another organisation.
"I think there's obviously a witch hunt. They have got to find somebody to take it out on.
"The players seem to be the ones locked into this and there's no wriggle room, whereas anybody else can point the finger further down the food chain or up the chain to the players."
Madden played 287 matches for Carlton after 45 games for Essendon. He later became a Labor MP and Victorian Sports Minister.
Essendon CEO Ian Robson resigned last week after accepting responsibility for errors made by the administration last season that had been highlighted by the Ziggy Switkowski report into club governance.
