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The charges were laid in the Queenstown District Court earlier this week in relation to the clearance of kanuka from a property in Hidden Hills Dr in May.
The land is owned by Allenby Farms Ltd. Director Brian Cleugh could not be contacted for comment.
It is the first time in at least five years the council has taken a landowner to court in relation to the clearance of native vegetation.
Queenstown Lakes District Council regulatory manager Lee Webster said the council investigated the clearance after receiving complaints from members of the public.
A significant amount of kanuka had been removed from an area that was protected by rules relating to significant natural areas and outstanding natural features, Mr Webster said.
"The council has an important role to play in protecting and preserving the district’s unique environment," he said.
A thorough investigation by the council had led to the charges being laid.
Council planning practice manager Blair Devlin said council provided advice for anyone wanting to check whether they needed resource consent for vegetation clearance.
Indigenous vegetation could be a potential fire hazard and the council took that into account when considering applications for resource consent to clear it, Mr Devlin said.