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The NZ Transport Agency has admitted the situation is ''below par'', and could carry on until next week.
Traffic was backed up along Castle St yesterday.
That meant traffic was also backed up on Anzac Ave as vehicles tried to turn right into St Andrew St, with reports of waits of 10 and even 15 minutes at that intersection.
The situation was exacerbated by cycleway work on Anzac Ave between the Dunedin Railway Station and St Andrew St, which has closed that section to traffic from the north.
An NZTA spokeswoman said last night a compounding factor was some traffic signal loops, or detectors in the road, had been damaged when new kerbs were built on Castle St.
That meant the Dunedin City Council and the NZTA's Wellington Transport Operations Centre (WTOC), which oversaw Dunedin traffic signals on the highways, had been monitoring the operation of the St Andrew St/Anzac Ave signals.
Adjustments had been made, and the Castle St/St Andrew St intersection was upgraded on Wednesday night with new poles, wiring and a controller.
The spokeswoman said that was the key intersection for co-ordination of southbound and State Highway 88 traffic, but detectors at affected intersections could not be reinstated until the lanes had been shifted.
''As a result, the co-ordination of traffic signals has been below par, a situation we are attempting to remedy as quickly as possible given the constraints.''
The NZTA hoped the traffic signal loops would be reinstated from next week at three intersections.
The WTOC would continue to monitor traffic lights during the morning peak today, and make adjustments when required.