A nuclear waste dump proposed for the Northern Territory will be on the agenda today when the Chief Minister meets with the Prime Minister.

The Federal Government says Muckaty Station near Tennant Creek is the only site under consideration for the proposed nuclear waste facility.

The Chief Minister, Paul Henderson, said federal legislation that imposes a nuclear waste dump on the Territory is exploiting a constitutional weak point.

He said he will voice his opposition to the dump when he meets with the Prime Minister, Kevin Rudd, today.

"This is too important a decision for the nation to take and the Commonwealth should go back to the drawing board," Mr Henderson said.

"Fourteen years worth of research that was conducted that identified 15 sites around Australia, none of which were in the Northern Territory.

"This decision should be based on science, not a constitutional weak point and I'll certainly be putting that case to the Prime Minister."

But Mr Henderson said he will not let the Territory's relationship with the Federal Government sour over the proposal.

"I have a very good relationship with the Prime Minister and other Australian Government ministers and I'm not going to let this one issue derail the relationship we have with the Australian Government," he said.

Mr Henderson also said he will not support the Federal Government's proposed changes to the health system unless they include additional funding for the Territory.

He said the unique circumstances in the Territory, including Indigenous health problems, need to be taken into account.

"John Howard over 11 years as prime minister ripped a billion dollars from the system," he said.

"[There are] significant problems and complexities with funding health in Australia and I will only sign up if there is additional funding for the Territory."

Mr Henderson is in Canberra for two days to meet with Mr Rudd and other federal ministers.