Warrnambool City Council will target fox "hotspots" in a spring baiting program.
Bait will be laid at Pickering Point, in vegetation behind the skate park at Lady Bay, Lake Pertobe and Thunder Point between September 26 and October 24.
Warrnambool City Council infrastructure director David Leahy said specially-trained border collie dogs had identified the hot spots.
"While the program aims to help all native wildlife, we are especially aware of the fragility of the Little Penguin colony on Middle Island," he said.
"(The) areas of fox activity around the island have been included in the baiting program.
"While we've had some success with baiting programs, the locations identified on the fox baiting map continue to be those of greatest concern and we will continue to focus on these areas."
Mr Leahy said the bait, PAPP, would be buried to make it attractive to foraging carnivores like foxes while protecting birds.
He said while ingesting PAPP could be fatal to cats and dogs that did not receive an antidote, secondary poisoning was "practically non-existent" for birds or animals foraging on the carcass of a dead fox.
Mr Leahy said signs of lethargy, loss of limb function, blue discolouration of the tongue and gums or any other uncharacteristic activity were symptoms of animals ingesting the poison.
"It (the animal) needs to be taken to a vet immediately as the window to effectively deliver the antidote is only about 60 minutes," he said.
The antidote is available at The Vet Group's Wollaston branch and Warrnambool Veterinary Clinic.
A detailed map of the Warrnambool fox baiting areas is available on the council's website or in hard copy at the Civic Centre at 25 Liebig Street.
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