A site near Hawker in South Australia's Flinders Ranges has been ruled out as the possible location for the federal government's nuclear waste dump.

Resources Minister Matt Canavan says after a ballot of local residents voted narrowly against hosting the facility, the site is no longer an option.

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"This ballot does not demonstrate a sufficient level of support and I will no longer consider this site an option for the facility," he said in a statement on Friday.

With two sites near Kimba, on South Australia's Eyre Peninsula, still being considered, the minister said he expected to make a decision on the preferred location early in the new year.

In the Hawker ballot, which closed on Thursday, just over 52 per cent of locals voted against hosting the dump on the Wallerberdina Station.

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A similar poll conducted on Eyre Peninsula recently returned a 62 per cent vote in favour of the idea.

And while both ballots were not binding on the Commonwealth, the results were expected to play a key role in the final decision.

Australian Conservation Foundation campaigner Dave Sweeney said the Hawker result also came amid clear opposition from regional pastoralists and the area's native title holders.

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"There is no broad community support for a national radioactive waste facility in the Flinders Ranges," Mr Sweeney said.

However, the Friends of the Earth said it was time for the federal government to abandon the dump plan altogether.

"The government has previously stated that 65 per cent would be a figure that would indicate the broad community support they need to select a site," spokeswoman Mara Bonacci said.

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"These ballot results show that the minister does not have that support."

The new dump will be designed to take Australia's low- to intermediate-level waste, with the government promising financial incentives to the community around the selected site.

Most of the waste material to be sent to the new facility comes from nuclear medicine.

Senator Canavan said while the Hawker site would no longer be considered, the federal government would still invest $2 million in the area through the community benefits fund.