Koalas suffering starvation were euthanised, while healthy koalas were released back into the wild and healthy females were treated with control hormone implants.
The cull is said to have occurred in secret to avoid a backlash from activists and locals.
Koala expert Dr Desley Whisson, who advised the government on the euthanasia program, stressed that the objective was to humanely deal with suffering koalas rather than reduce population size.
"Watching an animal starve to death is a horrible thing," Dr Whisson, from Deakin University, told Daily Mail Australia.
"For every one koala that was euthanised there were probably two or three that starved without intervention.
"It at least was a good thing to put them out of their misery."
Dr Whisson said moving the population to other areas or conducting fertility control programs were expensive options.
"A lot of people ask why we can't just move the koalas somewhere else, but I think it's important to recognise the translocation koalas often has a negative impact," she said.
"A large number would die, and they don't want to move from manna gum.
"It's sort of a lose-lose situation all round."
Dr Whisson said the problem in the manna gum woodland at Cape Otway was caused after koalas were introduced to the area in the 1980s from French Island.
"Manna gum is a very good food source for koalas, it's low in toxins and high in nutrients so koalas love it," she said.
"To the point where they don't move for the food supply.
"Koalas can move one or two kilometres in a night but in this population, they stay in these manna gum areas and numbers build up."
At Cape Otway there are up to 11 koalas per hectare, but the sustainable density is less than one koala per hectare.
Victorian Environment Minister Lisa Neville said she was putting in place a koala management program to deal with the 'a very challenging and complex issue'.
'It is clear it's an overpopulation issue and it is clear that we have had koalas suffer in "that Cape Otway area because of ill health and starvation," Ms Neville told ABC.
'That's just not good enough and that's a terrible way to treat koalas.
"I'm wanting to make sure that we're taking the best action we can in this terrible situation of overpopulation.
"I don't want to see koalas suffer."