Work has started cleaning up the old Waiuta mine site - described as New Zealand's most toxic contaminated site - in a joint $3 million operation.

Arsenic levels at the Prohibition and Alexander mines at Waiuta, south of Reefton, are among the highest recorded anywhere in the world at 400,000 parts per million on land - 500 times safe levels.

Decontamination work started at the ghost town last week. The road to the Prohibition Mine is now officially closed, downhill at Dingbat Flat. The access road to Big River remains open.

Department of Conservation acting conservation services director Roy Grose said the remediation work would start in April, with material from the nearby Alexander Mine site to be moved to the encapsulation pit at Waiuta.

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The $3.1m cost is being shared between DOC and the Ministry for the Environment. The clean-up was announced in 2013.

Mr Grose said the delay was a result of the further investigation required to "characterise" the Alexander site, review the plans and include the additional materials and review costs.

At the Prohibition site, the mullock heap had been absorbing arsenic and if its capacity was exceeded, the amount entering the environment, uncontrolled, would increase, he said.

"Arsenic levels close to the site in Coorang Creek are well above the levels acceptable for aquatic life."

The Alexander River site was on flood plain, and if the river changed course toxic material could potentially be washed downstream, he said. Excavated material from both sites will go into an encapsulation pit at Waiuta. The pit will then be capped.

The Prohibition Mine site was contaminated from the operation of a "roasting plant" involved in extracting the gold from the ore, from 1935 to the mine collapse in 1951. The entire town was later deserted.