State governments have their eyes on a potentially landmark native title case in the Northern Territory.

Native title holders in the town of Timber Creek, 600 kilometres south-west of Darwin, were awarded $3.3 million in compensation for the extinguishment of their native title rights late last year.

The case has now begun to assess if the method to determine the costs was correct.

The NT Government argues that it was not.

“The Government needs to make sure that this test case, being the first of its kind in terms of providing a compensation figure, is robust and will stand up to give us a test case into the future,” NT Attorney-General Natasha Fyles said.

“We've had conversations to ensure that the native title land owners understand the process, that it's not about disputing the claim, that it's simply understanding that process.”

The governments of Queensland, South Australia, and West Australia have intervened, keen to influence the state of play for groups in their states looking to file similar claims.

One key feature will be a determination of whether Governments have to pay compensation.

The appeal started this week, with three Federal Court judges hearing the NT Government's basis for its opposition.

Initially, more than $512,000 worth of compensation for the economic value of the land, over $1.4 million for interest, and $1.3 million for pain and suffering and the loss of cultural rights.

Justice John Mansfield described part of his decision as “intuitive”.

“Intuitive decision making in this context is not the appropriate way to make these decisions,” NT solicitor-general Sonia Brownhill said.

“Without referring to expert evidence there's no reason why [this amount] was selected as opposed to any other.”

Ms Brownhill wants the Government to take on a compensation formula from its own native title expert.

Meanwhile, traditional owners are lodging an appeal for more compensation.

Aboriginal groups from the Central Desert and Pilbara regions of Western Australia have joined the Timber Creek traditional owners' appeal as well.

The hearing continues this week.