The Federal Court has ruled in favour of traditional owners over miners following a five-year native title dispute in the Pilbara.

In 2007, the Ngarla people were granted a native title claim covering thousands of square kilometres of land and water in the East Pilbara.

But, there was a dispute over whether a mining lease had completely extinguished native title rights.

The full Federal Court has now ruled the Ngarla people do retain their native title rights on land when mining has ended.

The Yamatji Marlpa Aboriginal Corporation's Simon Hawkins says it is a significant win.

"What it's actually saying is that mining interests and pastoral interests are obviously leases, and tenements; they're not there forever and don't extinguish rights and interests," he said.

"So, that means when the mining activities ceases, which [they] will do at some point, the traditional rights and interests of the Ngarla people will then be able to be utilised fully again."

Mr Hawkins says it has been an arduous process.

"The other issue, which is quite frustrating, is that the State Government has pursued this matter and actually caused a lot of litigation around an issue that actually should not have occurred this way," he said.

The State Government says it is assessing the wider implications of the decision.