The first day of a five-week Federal Court hearing on Australia's proposed first nuclear waste dump has wrapped up in Melbourne.

A small section of Muckaty Station, about 600 kilometres north of Alice Springs, was put forward by the Northern Land Council (NLC) to store Australia's low and intermediate-level nuclear waste.

The waste is currently stored at Lucas Heights in Sydney before being sent to France.

The NLC nominated the site on behalf of members of the Ngapa group, but four other clans have laid claim to the land and say it is adjacent to a sacred site.

Those traditional owners have taken the council to the Federal Court.

"The Government, the Commonwealth and the Northern Land Council weren't talking to the traditional owners and they weren't consulted properly at the beginning," Dianne Stokes, one of the traditional owners to have their case heard in court, said.

Kylie Sambo from the Warlmanpa clan said the site sat in her grandfather's country.

"He left it for us to look after," Ms Sambo said ahead of today's hearing.

"It will definitely hurt our family because we've been fighting for so long ... we know what's in the country, we know what it means to us.

"For it (the dump) to be put there, it would be like killing our spirits."

In his opening submission today, their legal counsel, Ron Merkel, QC, told the court the NLC's consultation process was so legally flawed it was invalid.

He said the process had literally torn the Muckaty community apart.

When Justice Anthony North questioned him about whether there were any other sites at Muckaty that could be agreed upon, Mr Merkel said everything had been explored, but nothing had eventuated.

"We don't have the capacity to say what is available to the Commonwealth," he said.

"We only have the capacity to say the nomination [of Muckaty] is fatally flawed.

"What we are seeking is declaration that the nomination was not made in accordance with the laws."

*Dispute over compensation if dump goes ahead*

The Commonwealth has promised about $12 million in compensation to the Northern Land Council if the dump proceeds.

But Mr Merkel raised concerns about how that money could be spent, because it would go into a charitable trust and not to individuals.

"Not one Aboriginal person on the Muckaty Station has any right to one cent under this trust," he told the court.

Mr Merkel said the trust had unlimited scope and could even be used to set up Christian missions on the land.

NLC chief executive Joe Morrison said the Council had acted appropriately.

"I'm stating that the NLC stands by its processes in relation to all matters that relate to the court case and we believe that we've done everything properly, lawfully, and it was done comprehensively," he said.

The lawyer for the groups opposing the facility, Elizabeth O'Shea, said the case was about more than consent to use the land.

"It concerns burying radioactive waste on Aboriginal land and that throws up all sorts of questions about whether you can apply the same process of obtaining consent and to what extent you need to make extra effort to ensure people know what they're consenting to," she said.

"There's also some provisions about misleading and deceptive conduct, which is traditionally consumer protection, and we're alleging that the NLC was engaged in that behaviour."

Ms O'Shea said legal technicalities would also be tested during the case.

"Mostly I think it's interesting because the NLC is never usually put under this level of scrutiny and so we're ready to undertake that process and give traditional owners the opportunity to be heard," she said.

The Australian Conservation Foundation's Dave Sweeney says the value of the trial reaches beyond the Muckaty site.

"Muckaty is on trial in the Federal Court today but Australia's radioactive waste management needs to be on trial," he said.

"That's the big issue here for Australia - respect for traditional owners, but also the question of management of a long-lasting and industrial hazard."

The five-week series of hearings began in Melbourne today and will continue there tomorrow.

It will later move on to Darwin and to the site in question at Muckaty Station.

A decision is not expected until later in the year