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In April, the agency completed a $1.8 million project to resurface a section of State Highway 1, from Redcastle Rd to Virgil St.
However, in recent weeks, sections of pavement underneath the new surface have been slumping, and the agency is working with the Waitaki District Council to investigate what is causing it.
"We have been unable to trace the cause of the problem yet," NZTA senior network manager Chris Harris said.
"The site has been inspected by staff and our contractor has undertaken maintenance work to maintain safety and ride quality for the public.
"Once further investigations are completed we will have a better idea of what is happening to cause the slumping."
The pavement underneath the surfacing that had slumped was typically designed for a 25-year life, based on traffic loading and ground conditions, Mr Harris said.
"The overlying surfacing would normally last anywhere between eight and 16 years, dependent upon traffic stress - traffic volume, accelerating vehicles, braking, turning traffic - and oxidisation from UV/sunshine exposure," he said.
Temporary repairs have been carried out, and the road will continue to be monitored and maintained until permanent repairs can be completed.
Mr Harris thanked Thames Highway residents and motorists for their patience while maintenance repairs and further investigations were under way.