Several of the vaccine hesitant group, including players from Melbourne Victory, Macarthur FC, Western Sydney Wanderers and Perth Glory, could be stood down as early as next week.
Some, though, are seeking vaccine exemptions on medical - rather than moral  - grounds and have the support of their clubs and the Australian Professional League in pursuit of those waivers.
Victoria, for one, is mandating elite sportspeople to have had at least one inoculation by October 15. If they decline then they will be prevented from training or attending venues.
The players aired their concerns to the PFA on Thursday in emergency talks ahead of next month’s A-League kick-off.
Players union boss Beau Busch told FTBL: “As always, the PFA continues to have extensive consultation with its members on a range of issues, which includes COVID-19 vaccinations.
“The players across our professional leagues have complied with incredibly strict protocols and made significant sacrifices since the beginning of the pandemic to ensure the industry can continue to operate and to protect public health.”
Those who decline over freedom of choice issues face the prospect of having their contracts terminated, or possibly sitting out the season.
They believe they are being coerced into taking what they believe is a rushed vaccine with an unknown long-term safety profile.
Both the PFA and the clubs are in favour of the mass nationwide vaccination program and are encouraging the players to reconsider.
“Following an extensive education program delivered with the APL and the clubs vaccination rates have to date been incredibly high and we continue to ensure that players have access to medical advice and expertise as required," addedd Busch.
“As the health advice and measures across the country continue to evolve we are continuing to assess the impacts on players in relation to their COVID-19 vaccination status and ensure that players are provided with the best possible information and advice.”