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.