On Tuesday a Federal Court granted the claim, one of the nation's largest, covering more than 193,000 kilometres from Hopetoun in the south to north of Jurien Bay, excluding Rottnest Island.
Federal Court judge MURRAY WILCOX declared the indigenous Nyoongar people as the traditional owners of the area across the state's south west, including Perth.
But Mr Howard said it appears at odds with another important ruling and he’ll be seeking more advice on the issue.
That will include whether the federal government should join an appeal flagged by the Western Australian government.
He also said the ruling appears at odds with aspects of the High Court's findings in another important native title case the Yorta Yorta claim in Victoria.
Appeal likely
Federal Opposition Leader Kim Beazley earlier said it’s likely the Western Australian government will appeal the native title ruling.
The Western Australian government has already signalled that it will appeal against the federal court decision.
Historic ruling
Lawyers said that the landmark judgement is the first time a large metropolitan area in Australia has been ruled to belong to the indigenous people who lived there before white settlers arrived.
It could lead to similar claims over other cities such as Sydney and Melbourne, native title specialist Christine Lovitt told AFP.
Homeowners and businessmen holding freehold title to their properties were assured that the ruling by Justice Murray Wilcox did not mean they could be evicted.
Justice Wilcox said the decision to grant native title was "neither the pot of gold for the indigenous claimants nor the disaster for the remainder of the community that is sometimes painted".
Ms Lovitt said a likely appeal process by the government of West Australia could take years.
Justice Wilcox found that the Nyoongar people had proven native title existed over Perth by continuing to observe traditional customs despite being largely dispossessed by white settlement in 1829.
"The outcome was probably a little surprising for most people because one would have thought in a highly developed area that the native title claimants would probably have lost their connection to the land," Ms Lovitt said.
Native title is, however, "extinguished" by the granting of freehold title, she said.
Aborigines welcome decision
Aboriginal leader Noel Pearson said the "absolutely extraordinary" decision by the court restored native rights to Aborigines who lived in the cities and southern regions of Australia.
"Native title is not the preserve of the most traditional groups in northern and remote Australia, it is also the legal right of people in urban and southern Australia."
Aborigines have lived in Australia for at least 40,000 years, but they are now a minority with a population expected to reach 470,000 this year out of a total of 20 million.