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The culvert on the Dunedin-Port Chalmers Rd, near Ravensbourne, had started to slump last week, the agency said.
Senior network manager Chris Harris said repair would take several weeks given the number of key services that were contained in the area, such as water, power and drainage.
"We will attempt to keep the highway open to two lanes at peak hours and other times wherever possible with a reduced speed limit."
Crews needed to undertake a trial later this week to decide whether ground conditions would be suitable for new pipes, Mr Harris said.
The route was of "critical" importance to the port and there was a need to keep it open to two-way traffic as much as possible given the lack of a detour.
"We have had a number of people from different organisations involved in this work ensuring their key assets which pass in close proximity to this culvert are protected — from Aurora, from Delta, from Dunedin City Council’s three waters team, as well as our own highway repair crew and a structural engineer managing the retaining wall repair.
"We thank all road users and residents for taking care around the large number of workers involved in this complex repair and their continuing courtesy as we work to reinstate this critical link to the West Harbour area."