The woman, aged in her 60s, was at Three Mile Creek in Wyndham, about 3,200 kilometres (2,000 miles) north of Perth, on Wednesday afternoon when the croc lunged, Western Australia's Country Health Service told AFP.
She was flown to the Royal Darwin Hospital in neighbouring Northern Territory in a stable condition, and underwent surgery late Wednesday, St John Ambulance NT operations manager Craig Garraway said.
"She was beside a very small creek 300 metres down from our Five Rivers Cafe on the Great Northern Highway... At some stage, a crocodile came out and attacked her," cafe owner Michael Snowball told AFP.
During a death roll a crocodile spins and twists to rip off parts of its prey.
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Snowball said it was the first time he had heard about a crocodile attack at the creek, just three metres wide and 1.5 metres deep, where children swim during the wet season and fishermen regularly catch live bait.
Police cordoned off the area but by the time wildlife officers arrived, the animal could not be found. A Department of Parks and Wildlife spokeswoman said the creature was believed to be a saltwater crocodile, which can grow up to seven metres (23 feet) long and weigh more than a tonne.
Crocodiles are common in Australia's tropical north where numbers have increased since the introduction of protection laws in 1971, with government estimates putting the national population at approximately 100,000.
They kill an average of two people each year in Australia.