Members of the Wangan and Jagalingou people have been fighting against the mining company, claiming they did not give permission for the $16.5 billion mine to go ahead.

In the federal court in Brisbane on Friday, Justice John Reeves ruled in favour of Adani, and ordered the indigenous group to pay the mining company's costs.

Wangan and Jagalingou representative Adrian Burragubba says it's a disappointing result.

"Our position has always been the same - that there has never been any free or informed consent with any agreement with Adani," Mr Burragubba said outside the court on Friday.

The Wangan and Jagalingou people are divided over the mine.

Adani has struck a deal with some of the traditional owners, while others say they never agreed to it.

Mr Burragubba is the leader of that group and says they will take the matter to the High Court.

They have pleaded with the Queensland government to hold off on handing native title rights to Adani until they make a High Court challenge to the ruling.

"We don't want them to surrender Native Title in the area where the airstrip and the camp (for the mine) would be," Mr Burragubba said.

"So we're asking the state not to compulsorily acquire that land while there remains a legal question ahead of us."

Once Native Title rights are extinguished on the land they cannot be regained, which Mr Burragubba says was not explained by Adani at a meeting with indigenous owners in 2016.

Adani welcomed the court's decision.

"Following today's decision we look forward to working with the state government and the traditional owners to finalise land tenure for the project," it said in a statement.

Securing the Indigenous Land Use Agreement is one of the final hurdles for the beleaguered mine project and has hindered its efforts to secure international financing.

Australian Associated Press