The green turtle was brought to Sydney from the Hunter region of NSW just over a week ago, after it was found caught in netting attached to a fishing pot.
"It's also got damage to the side of its mouth - we think there must have been line going into its mouth, and … there's evidence of a fish hook caught in its neck," Dr Frances Hulst, veterinary officer at the wildlife hospital said.
The veterinary team used an X-ray to identify the hook, and found fishing line had cut its flipper causing tissue damage to the bone.
The team were unable to extract the hook from the turtle during surgery, but don't believe it will cause further damage.
While the turtle had a "dramatic wound" on its flipper, Dr Hurst said she was hopeful it would heal.
"I think the turtle will always have a defect in that limb, but if it's functional and she can swim with it then that's what we really want."
The turtle is now recovering in intensive care, and is eating squid and swimming.
One of the challenges of treating sea turtles is their size and weight – with species able to grow to over 100kg.
"This animal was only 31kg, but a pretty solid lump," she said.
The wildlife hospital treats many different species including amphibians, birds, mammals and reptiles, Dr Hurst said, adding the clinic has to be "very adaptable".
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