The rabbit died soon after. The veterinarian said the rabbit had either been hit or kicked with a lot of force.
In February the business, which allows tourists to play mini golf while patting the pigeons and rabbits, found the birds had been stolen.
"There was a heap of feathers around and a hell of a mess, I found a couple in the bush, a guy across the road found four of them behind his shed [by] a little fire. Their heads and their feet had all been chopped off."
Mrs Duncan said two weeks ago she found large rocks thrown all over the greens and another rabbit (Coco) was dead.
"He was 2-and-a-half, we rescued him from the SPCA. Him and [another rabbit] Marbles had become really good buddies. They slept together and chased each other around, they were really good mates."
She said that Marbles was "out of sorts" for the next couple of days and would hide from the staff.
The manager said staff didn't lock the rabbits up at night because they used to sleep by each other but now they are considering taking the last remaining rabbit home for its own safety.
All of the staff at Mini Golf New Zealand were "devastated" by the incidents, Mrs Duncan said.
"We'd have customers coming in and we'd burst into tears. They'd sort of look at you and say 'oh we're really sorry'."
Mrs Duncan said they had reported the incidents to the police who had given them some security tips.
"We now have CCTV cameras and we are asking anyone who may have seen anything suspicious to contact us or call the police."
She said the business was torn whether or not to continue having animals on site.
"We get a lot of visitors from Australia ... They love interacting with the animals. So we don't want to get to that stage of not having animals on the site but we may have to consider it."