A noisy protest on Darwin's main wharf is calling for the federal government to rethink plans on a nuclear waste dump in the Northern Territory.

Shouting "Don't waste the territory, dump the dump now", about 100 people voiced their anger at plans to build the proposed nuclear waste dump at Muckaty Station, about 100km north of Tennant Creek.

The protest was organised by the Maritime Union of Australia, which in March passed a resolution supporting traditional owners of Muckaty who are against the waste dump.

Some nuclear waste bound for Muckaty will likely pass through Darwin's wharf where MUA members may be expected to help transport it.

"I implore you all to keep the fight going," said MUA Victorian branch secretary Kevin Bracken.

Lorna Nangala Fejo, who identifies as one of the Stolen Generation and is originally from Tennant Creek, called on the government to abandon the planned mine at Muckaty.

Isobel Phillips, a traditional owner from Muckaty, said she would do whatever she could to stop nuclear waste reaching the proposed dump site.

"I will block the road. I don't care if I get arrested," Ms Phillips said.

"I don't care if I get run over," she said.

Another traditional owner from Muckaty, Bunny Nabarula Warramunga, said she thought the fight to stop the dump would eventually be won.

"I just want them (the government) to listen to us," Mrs Nabarula said.

Nuclear campaigner at Environment Centre NT, Cat Beaton, said workers were concerned about dangers from transporting radioactive goods.

"We are also concerned for the health of the Darwin Harbour and don't want nuclear waste crossing it," she said.

A federal court challenge to the proposed waste dump is under way in Melbourne.

Federal Indigenous Health Minister Warren Snowdon earlier told journalists there was no guaranteed outcome on what would happen at Muckaty.

"If the court determines that things haven't been as they should be then the site won't go ahead, but I am not going to be interfering in that process," Mr Snowdon said.