In 2013 Glencore applied for a mineral lease for the McArthur River mining project, with plans to build a facility on land to deposit sediment dredged from shallow gulf waters to allow bulk-carrier vessels to ship the mine's ore.
Though Glencore owns the pastoral lease for the land, it is subject to native title.
The Northern Land Council and two native title holders have successfully upheld their freeholder and procedural rights to negotiate under the Native Title Act, forcing the company to come to the table and work on an agreement with them.
The High Court on Wednesday unanimously overturned a Federal Court judgment that the new infrastructure facility was too "remote" from mining and could not be regarded as "necessary for the meaningful exercise of the right to mine".
High Court justices Stephen Gageler, Michelle Gordon, Simon Steward and Jacqueline Gleeson ruled the granting of the mineral lease would be a "right to mine" under the Mineral Titles Act.
Also an infrastructure facility was covered by the Native Title Act and the appellants were entitled to their rights under that legislation.
Glencore general manager Mark Furlotte said the company respects the High Court decision.
"McArthur River Mine continues to be engaged in discussions with the traditional owners and with the Northern Land Council in relation to the land which is the subject of the decision of the High Court and other matters," he said in a statement.
The McArthur River Mine was established in 1992 and is one of the world's largest deposits of zinc and lead.
The mine, almost 750km southeast of Darwin, has been dogged by environmental incidents and claims sacred Indigenous sites face irreversible cultural and ecological damage from its operation.
Last year traditional owners went to the Federal Court seeking "no less than" $225 million in compensation for environmental and cultural damage from the mining operations.
The court will hand down a decision by December.
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