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Port Otago chief executive Geoff Plunkett said work repairing the mole using rock from a nearby quarry began last month.
More than 10,000 tonnes of rock would be placed on the earthen breakwater to repair damage caused by normal tidal erosion and recent easterly storms, he said.
Port Otago spent about $40,000 on maintaining the mole each year.
In 2002, 17,000 tonnes of rock was blasted from a nearby quarry to repair damage that had occurred that year, at a cost of about $200,000.
Concrete tetrapods placed at the end of the mole some years ago had also gradually shifted on the western side of the breakwater.
The mole was important for alignment of the shipping channel at the mouth of Otago Harbour and improving tidal flow, which maintained channel depth, Mr Plunkett said.
The mole was constructed in the 1880s and material was added in 1961 to bring it to its current height.
Last century, derelict ships were scuttled alongside the sea wall to offer additional protection.