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The AFLPA has raised concerns with the league over a requirement for Indigenous players to have a pneumococcal vaccination before entering a quarantine hub.

The AFL has apologised to Aboriginal and Torres Strait Islander players over a communication bungle in relation to a vaccination they may require.

All players had needed to have flu shots before entering a Queensland Hub, but concerns have been raised over the extra requirement of a pneumococcal vaccination for Indigenous players.

The AFL Players Association took the league to task over the move.

"In the past 48 hours, the AFLPA has become aware of Indigenous players being required to have pneumococcal vaccinations prior to entering AFL (hubs)," AFLPA chief Paul Marsh said on Saturday.

"We are very concerned about this issue.

"The fact that these vaccinations were not discussed with the AFLPA as part of the return play protocols or otherwise, is a significant issue we have raised with the AFL.

"We are now working directly with players to ensure they understand their rights and options available to them regarding any requested vaccinations."

The AFL issued an apology later in the day for their failure to notify the appropriate parties about the vaccination earlier.

"The AFL apologises to Aboriginal and Torres Strait Islander players and staff and the AFLPA for not providing sufficient clarity around Aboriginal and Torres Strait Islander players receiving a pneumococcal vaccination ahead of entering Queensland and for any distress this has caused them and their families," the statement said.

"The AFL acknowledges it could have obtained and shared more information from the Queensland Government health authorities regarding the vaccination including the underlying health safety benefits and that it can improve its processes in providing information to support club doctors in ensuring cultural safety in provision of health to Aboriginal and Torres Strait Islander peoples.

"The AFL is committed to working closely with the AFLPA and the players, our clubs and our doctors to resolve the situation."

It remains unclear what will occur if a player rejects the extra jab.

Players inside hubs are subject to strict coronavirus mitigation protocols, put in place by the AFL, and are regularly tested.

The AFL is relying on teams to enter isolation hubs to keep the season going as the global pandemic continues.

Victorian clubs had been promised they would be away from home for a maximum of 32 days but the league is working with the AFLPA to extend that out to as much as 10 weeks as a result of the state's worsened COVID-19 situation.