Lee Gaskin, a reporter working for the AFL in South Australia, revealed the game's governing body deemed Mouncey's "physical disparity is significant and would give unreasonable advantage".
Despite being denied for 2018, there is a chance Mouncey will be accepted for the 2019 season.
Mouncey previously represented Australia as a male in European handball.
Footy journalist Sam McClure said the AFL based its decision on the Victorian Equal Opportunity Act, which states athletes can be discriminated against based on their sex "if strength, stamina or physique is relevant".
AFL General Manager, Inclusion and Social Policy, Tanya Hosch thanked the 27-year-old for her understanding.
"Hannah's passion for football is undeniable, and I want to thank her and her team for their constructive participation in the decision-making process," she said in an AFL media release.
"It was important to involve the right stakeholders to review all the information and data available. Every case will be decided on its own merits along with the individual circumstances of each future nominee," Hosch says.
"We acknowledge Hannah's openness and co-operation. She has contributed to a process which will substantially inform the development of the AFL's transgender policy and procedure for future players at the elite level."
"The AFL has made very strong commitments to equality and inclusion at all levels of the game. We recognise that participating in sport has physical, psychological and social benefits and we are committed to making Australian football on every level welcoming to all in our community."
'IT COULD GET QUITE MESSY'
A leading Australian media lawyer says the AFL is in danger of being accused of discrimination for the polarising decision to deny Mouncey a spot in the league.
The 190cm, 100kg ruck played eight games for Ainslie in Canberra's women's competition this season and kicked 17 goals - but AFLW clubs are still unsure if they will be able to recruit her through the AFLW draft.
Having previously played for Australia's men's handball team, Mouncey began taking gender transition hormones in 2015.
Melbourne-based lawyer Justin Quill on Tuesday warned the AFL it will leave itself open to a "messy" legal challenge if it denies Mouncey accreditation as a sanctioned AFLW footballer.
"If they don't it could get quite messy and quite complicated if they go the other route," Quill told SEN's Breakfast on Tuesday.
"I think they will allow her to play. I think her levels that she's tested at, as I understand it, you guys just talked about the IOC guidelines, she's well, well within the testosterone levels that the IOC will allow and I think they (The AFL) will rely on that.
"They will use that. I also think they will develop a policy for future cases."
He said the IOC precedent means there is little scope for the AFL to try to block her inclusion if they decide Mouncey should not be allowed to compete.
"That's going to be very difficult for them to do and that's why I think they will allow her to play," Quill said.
"They could say, 'She's too big. She's too strong. Her strength and stamina et cetera is greater'. They could try and say that, but I don't think there really is much of a basis because if they don't allow her to play I think there is a reasonable chance that they could be facing a legal challenge and I'm sure there are bodies out there that would support her to make such a challenge.
"She would say, 'I've been discriminated against because of my gender'. In the eyes of the law, she would say, 'I'm a female and I should be allowed to play and you're not allowing me to play and therefore I'm being discriminated against'.
"That will be very much in the minds of the AFL when they make their decision."
The AFL follows International Olympic Committee rules which state an athlete must prove their testosterone count is below a certain level.
It is understood Mouncey meets those requirements.
Inspired by the success of the inaugural AFL Women's season, Mouncey has previously spoken of her desire to test herself at the highest level. But she took to Twitter on Monday to decline further comment. "At the moment I am not in a position to make any comment surrounding my availability for the draft," Mouncey wrote.
"(I) will not be doing any interviews or making comment on the situation."
- with AAP
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