Dispersal of the Kareela grey-headed flying fox colony started on Monday August 3.
Sutherland Shire council hired a contractorto disperse the estimated 7000 bats in the colony, although their numbers have been as high as 18,000.
The move has the approval of the NSW Office of Environment and Heritage (OEH) and the Department of Environment.
It could cost up to $850,000 and is expected to take until the end of August.
An independent ecological expert approved by the OEH will monitor the work which will include noise, ultrasonic devices, smoke, light and physical disturbance to stop the bats returning to roost.
The colony is affecting the grounds of the nearby Sylvanvale Mikarie Child Care Centre, which cares for more than 150 children aged up to six including children with disabilities, and the Bates Drive Public School and Aspect South East Sydney School.
Flying foxes are flying low over the outdoor play area of Sylvanvale during the day, leaving faecal droppings on play areas and equipment. Teachers have had to evacuate the playground several times.
NSW Health said there is no health risk for humans from the flying foxes provided they are not scratched or bitten.
If a scratch or bite does occur, the wound should be washed immediately with soap and water, and medical advice sought.
A small percentage of flying foxes may carry the Australian bat lyssavirus.
But residents are still advised not to approach the flying foxes.
The flying foxes feed at night and will be visible flying around even if the dispersal is successful.
Sutherland Shire mayor Kent Johns asked residents to inform the council if they see flying foxes roosting in new spots during the day.
Daytime sightings of flying foxes can be reported via the council website www.sutherlandshire.nsw.gov.au.
Would you like to see the bats stay or go?