The female joey was found Friday at Jimna, west of Queensland, with 15 shotgun pellets lodged in its body and skull.
The koala had emergency surgery, but veterinarians could only remove three of the pellets.
It is believed the mother may also have been shot, but its body has not been found. The penalty for deliberately shooting a koala is a $225,000 fine or two years in jail. Authorities are searching for the person or persons who shot at the koala and are appealing to the public for information.
The Koala is one of Australia's signature animals. The small marsupial lives in the interior regions of the eastern states of Queensland, New South Wales and Victoria.
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