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New Zealand Transport Agency (NZTA) senior asset manager John Jarvis said the bridge's structural steel was being corroded and, while it was not an immediate safety risk, action was needed to reduce the 400-strong flock of resident pigeons so damaged areas could be repaired.
The corrosion mostly affected the surface, but there were also some cases of pitting.
The need to clean the walkway over the bridge had increased significantly in recent times and that was a health and safety issue.
"At the moment, the priority is to clean it up. It's a horrible job; health-wise it is very dangerous.
"Until we clean it out, we can't get a good idea of the damage but the longer we put it off, the more it will cost.
"There are lots of little nooks and crannies and that's where they have been roosting over the years and dropping excrement," Mr Jarvis said.
The agency had settled on a plan of attack, which will use an anaesthetic-laced bait, after consultation the Central Otago District Council, Department of Conservation, Otago Regional Council, SPCA, and the New Zealand Forest and Bird Society.
From next week, agency contractors will begin to lay non-laced bait. Then anaesthetic-laced bait would be offered, which would make the birds drowsy, allowing the contractors to catch them and humanely kill them.
Mr Jarvis said they were confident other birds would not get caught up in the culling but if they did, there were people on site who would be able to "bring them back to life".
Though the agency, at the request of the SPCA, was advising pet owners in the area to keep their animals away from the bait, Mr Jarvis said he was confident there would be no problem.
He said it was a "tried and true" method that had been tested at other places around Central Otago, including the Victoria Bridge in the Kawarau Gorge and a couple of other bridges in Maniototo.
It is hoped the operation to kill all the pigeons will take between five and seven days. It is expected to cost just under $4000.