"Haddin has been ruled out of the remainder of the Carlton Mid ODI series (against South Africa)," Cricket Australia said.
Haddin badly injured his shoulder while doing wicketkeeping duties in Australia's 0-2 Test series defeat at the hands of Pakistan in the UAE.
And Hadding is battling to be fit on time for the first Test against India at Brisbne, starting December 4.
"Brad has had a further assessment of his right shoulder by Cricket Australia Chief Medical Officer Dr John Orchard which confirmed an AC joint injury," Kountouris said in a statement
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"Therefore he has been declared unfit for the remainder of ODI series against South Africa," he said.
"While Brad will miss the ODI series the CA medical team is still hopeful that he will recover in time for the first Test against India," the physio added.
Australia coach Darren Lehmann, a member of the four-man selection panel, stressed that Haddin will requite to prove his match fitness to be considered for a berth in the Test team.
"He would have to play some cricket before the first Test starts," Lehmann said.