The Ospreys second rower is hopeful of returning before Christmas after surgery this weekend but will also miss the Welsh side's upcoming Heineken Cup fixtures, starting with Treviso on Saturday.
Ospreys head physiotherapist Chris Towers said: "Alun Wyn suffered a foot injury in training this week and as a result, he is going to require surgery to repair soft tissue damage, which will be carried out over the weekend.
"Once he starts his post-op rehab work we will be in a better position to predict recovery timelines."
Ospreys teammate Ryan Jones meanwhile is favourite to replace his stricken namesake for both clashes against Treviso and Australia respectively.
Gatland, who names his 26-man squad for the Millenium Stadium showdown on Sunday, is also sweating on the fitness of Dan Lydiate and Justin Tipuric but will definitely be without Perpignan fly-half James Hook because the game is not an IRB sanctioned game.