The Northern Territory Chief Minister says he will use local legislation banning the transport of nuclear waste to prevent the Federal Government from building a radioactive waste dump in the Territory.

The Rudd Government yesterday revealed it would pursue Muckaty Station, near Tennant Creek, as the location for a national radioactive waste repository.

It says it has to find somewhere to store nuclear waste generated by the creation of medical isotopes at the Lucas Heights reactor in Sydney.

Prior to the 2007 election, the federal Labor Party promised to repeal Howard government legislation which allows the Commonwealth to bypass Territory laws and force a nuclear dump on the Territory.

The Rudd Government says it intends to follow through with that promise despite yesterday outlining its intentions for Muckaty Station.

It says Muckaty Station is the only site in Australia that has been "volunteered" by traditional owners via the Northern Land Council, although it acknowledges that not all of the traditional owners are supportive.

The Country Liberal's MLA David Tollner says if the Commonwealth act no longer exists then the Territory's Nuclear Waste Transport and Storage Bill would come into place, making it illegal to bring nuclear waste into the Territory.

The Chief Minister, Paul Henderson, says his Government will try to use the local legislation against the Rudd Government.

"If they do repeal the act as it stands now, our legislation will be in play and it will stay in play until we have a proper robust debate nationally based on the science," he said.

The Australian Conservation Foundation's Dave Sweeney says the Rudd Government is breaching international best practice by keeping Muckaty Station as an option.

"There has been a decision that Muckaty is the most politically-expedient option," he said.

"Minister [Martin] Ferguson should have torn up the Muckaty option should of gone back to the drawing board and should of done what Labor promised to do, which is a new site selection option based on good science, good policy, community inclusion and consent."

The Northern Territory Labor MLA for the area being considered for the waste storage facility says the views of some traditional owners are not the views of his electorate.

Gerry McCarthy says the views of those traditional owners are important but everyone else in his electorate is against the idea.

"That's one side on the table and I think there is a lot more of the debate to come.

"The debate is one of science, one of national security and of a facility that will be the first in Australia and needs to be done very, very carefully."