The government of Western Australia said it would launch the appeal despite warnings from Aboriginal community leaders that it would set back relations with Australia's native people.
The federal court ruled on September 19 that the Noongar people had proven an unbroken connection with more than 6,000 square km covering Perth and the surrounding area despite being largely dispossessed by white settlement in 1829.
Native title is a collection of rights rather than a direct title for the land, and does not affect the rights of other people living in the area.
Eric Ripper, Western Australia's deputy prime minister, said the standards for native title used in making the ruling were radically different from previous decisions.
"A clear and consistent understanding of native title law provides a guide for the settlement of all native title claims by agreement," he told reporters.
Western Australian officials will meet leaders of the Noongar Aboriginal community in an attempt to negotiate a deal, Ripper said.
"The government wants to ensure a very good outcome for Noongar people in Western Australia through this process," he added.
The national director of Australians for Native Title and Reconciliation, Gary Highlandsaid, said the appeal was a waste of money and would tarnish a great victory.
"The attitudes of both the federal and the WA [Western Australia] government have been extremely disappointing in relation to this matter. Native title is no threat to non-indigenous people in Australia." he said.
About 400 people gathered outside the state parliament on Thursday to protest against the move.