Speaking at the opening of Australia's first helium plant outside Darwin, Mr Ferguson said it was unacceptable that nuclear waste was being stored in filing cabinets and shipping containers at Australian hospitals and universities.

"If you want nuclear medicine, if you want a reactor in Australia that produces 85 per cent of our nuclear medical requirements, then you have to accept the responsibility to store the waste," he said.

Mr Ferguson said 500 Australians a year sought access to nuclear medicines and Australia had a responsibility under international protocols to set a national repository to store its own nuclear waste.

The government is considering a site at Muckaty Station, 100km north of Tennant Creek, that was nominated by the Northern Land Council more than two years ago in a deal with the Howard government.

If the deal goes ahead, a $12 million trust fund will be established, $1m of which is slated for education services for local people.

Mr Ferguson said he had not imposed a site and that it had been a voluntary process with the site's traditional owners, the Ngapa people.

Territory Chief Minister Paul Henderson reaffirmed his opposition to the proposed site and said studies in 1992 and 2004 found several interstate sites could house the project.

Mr Ferguson welcomed the $50m helium plant at Wickham Point. Operated by compressed gas supplier BOC, the plant is the first in the southern hemisphere and will replace imports from the US and the Middle East, with two thirds of production to be exported to Asia.