Computerised recordings of loud industrial noise and banging sounds have been blared twice a day since last Monday in an attempt to displace the 5000 strong grey-headed flying fox colony.
Bat numbers were down to 150 last Friday and executive director of the Royal Botanic Gardens & Domain Trust Dr Brett Summerell said that by Monday the population had dropped to only 10.
"The majority of bats have been evicted from the gardens," he told AAP on Tuesday.
"We've been playing a range of industrial type noises - basically annoying sounds for about 45 minutes in the mornings and 35 minutes in the evening," he said.
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 botanical gardens will now focus on repairing trees damaged by the bat colonies and planting a new collection of palm trees.