However, bat advocacy groups say more bats are expected to roost around September and October because of seasonal movements.
Bat Watch's Nick Edards said the bats are simply moving on to Centennial Park.
"The number of bats there has increased ... so it seems they've moved there [from the Gardens]."
Dr Summerell said bat colonies did exist in Centennial Park but the bats removed from the botanical gardens had been tracked moving around the state.
"They're dispersing around the Sydney region, up the coast, all the way up to Queensland," Dr Summerell said.
"From the satellite tracking, we've seen they're moving to a whole range of colonies, not any particular location."
The botanic gardens will now focus on repairing trees damaged by the bat colonies and planting a new collection of palm trees.
- AAP