But after inspecting damage to dozens of trees they now believe there are twice as many as previously thought. Branches have been snapping under the weight of these furry invaders and their droppings are poisoning plants.
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Officials at the Royal Botanic Gardens have said they are optimistic the unwelcome colony can be uprooted - perhaps with the help of the humble dustbin.
The botanic gardens' executive director Tim Entwistle hopes the jarring sounds of crashing bin lids will agitate the flying foxes and force them to move on.
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"The way to disturb them is to use noises, so we've used banging of rubbish bins in the past," he said. "But you can also use speakers as long as you move the noise around."
He says he hopes two weeks of noise should encourage the flying foxes to go elsewhere. If and when the bats do move on to other parts of the city they will of course then become someone else's problem.
There's a photo gallery here.
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