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Ministry general manager commercial and property Fraser Gibbs said the viburnum hedges outside the Dunedin District Court had been infected by thrips, small insects that survive by sucking sap out of plants.
The ministry had been aware of an issue with the plants since March, he said.
Specialised gardeners had been engaged to remove the infected plants and replace them with a hardier plant called Sophora Dragons Gold, a type of kowhai.
There were plans to replenish the garden areas with more compost and soil, and to install a basic irrigation system to the affected side of the courthouse, he said.
There was no timeline for the work yet as cost estimates were still being received, a ministry spokesman said.