The Northern Territory Government's fight against a national nuclear waste facility in its jurisdiction has taken a massive blow with a peak Indigenous group describing the Government's position as irrelevant.

The organisation representing traditional landowners in the Top End says it wants to suggest a new site for a nuclear waste dump in the Northern Territory.

The announcement flies in the face of the Territory Government's commitment to oppose the facility at all costs.

Legislation currently before Federal Parliament paves the way for the facility to be built at one of three sites identified by the Commonwealth.

But the Northern Land Council (NLC) says its 78 members have unanimously voted in favour of an amendment to the legislation so it can nominate a fourth site outside the existing three already ear-marked.

The NLC says it wants to suggest a new location, as long as traditional owners agree and sacred sites are protected.

The council has also slammed the Territory Government's handling of recent debate about the waste dump.

The council's chief executive Norman Fry says the NLC recognises the facility is of national significance and says it seems inevitable that it will be put in the Territory.

He says the NLC represents 23 per cent of the Territory's land mass and wants to be pro-active in getting the best deal for traditional owners.