Australian Athletes Alliance chief Brendan Schwab has urged the AFL to establish an independent body to adjudicate on major decisions.
The role of the AFL Commission was questioned last year after it determined the penalty on Essendon Football Club and coach James Hird for governance breaches, having also brought the charges.
The AAA - which has the AFL Players Association as part of its constituency - wants an independent panel introduced for hearing potentially serious breaches of conduct.
"We think there needs to be a strong separation, say, between the board, which is the policy-making body, the executive which administers the competition, and the judiciary which determines disputes," Schwab said. "We think all sports should guarantee that, and it's in their own interests to do it because their procedures will be more legally robust and fairer."
In its policy paper, the AAA said: "Well-governed sports have a clear separation of powers between the board and general meeting [legislature and governance], the executive [administration] and the judiciary [determination of disputes].
"They have a clearly defined alternative dispute resolution policy, which includes giving athletes the right to an independent and accessible disciplinary and grievance tribunal in which athletes have an equal say with management in the composition of the grievance tribunal."
The AFL declined to comment.
The AAA has also released a 15-point charter of rights with which it wants all major sporting competitions to adhere. This includes the right for players to have a sporting environment that preserves the integrity of the code, is a safe workplace that resolves disputes "through impartial and expeditious arbitration", and one that allows an athlete "the right to freedom of opinion and expression".
Schwab revealed the likes of the AFLPA and the Australian Cricketers Association would challenge the AFL and Cricket Australia on the charter.
"All of our player associations are in the final phase of preparing a compliance report on where their sports are in terms of compliance with the charter and policies, and we will then ask each of our associations to take that up with the relevant sports to ensure compliance," he said.
In terms of the medical health of players, Schwab said it should be mandated that players have a right to a second medical opinion by a doctor of their choosing. That second opinion - outside of the club - would then "prevail" unless unreasonable.
"We think that is fairly basic and is something that is mandatory, for example, under the rules of FIFA that a player has a right to a second medical opinion. We think it's very common in the sports in the world," he said.
"We had to fight hard for that in football [soccer], but now it's well established. Again, it ensures greater transparency and accountability in the medical treatment of players.
"We have even seen in the recent World Cup in Brazil that there can be [with] team-appointed doctors a lack of independence on critical issues such as concussion."
While the AFL has beefed up its concussion protocols, there are still questions about whether enough is being done. The AFLPA is pushing for independent medical advice to determine the fate of concussed players, with lower-end concussion cases a particular issue.
The AAA also said players must not be given injections other than by the team doctor or other medically qualified practitioners, and that genetic testing must be prohibited.
Schwab said he had no knowledge of genetic testing being conducted, rather it had been listed as a "policy position".