The young koala was critically injured with a fractured skull, damage to its stomach and severe blood loss.
Veterinarians have named the koala Frodo.
Authorities promised to track down whoever shot the young animal.
"We're going to throw the book at these people. If we find them, they will face up to two years imprisonment or over $200,000 in fines," said Kate Jones, Queensland sustainability minister.
The baby koala had surgery to remove several pellets, but she'll need more procedures.