ELEANOR HALL: Victoria's Environment Minister has admitted that the previous Napthine government ordered the killing of almost 700 koalas in a secret cull along the state's Great Ocean Road.

She justified the cull on the grounds that the animals were starving due to over-population.

But the Koala Foundation is outraged and claims the Victorian Government colluded to ensure the animals didn't attract protected status.

Rachael Brown reports.

RACHAEL BROWN: The woodlands at Cape Otway, south west of Melbourne, is home to one of Australia's largest koala colonies.

But up to 8,000 koalas have been crammed in and they're eating each other out of house and home.

They've been stripping manna gums bare, meaning the weakest koalas - the oldest and smallest - don't survive.

So Victoria's previous Coalition government decided to cull 686 of them.

DESLEY WHISSON: I witnessed animals starving to death and it's just not pleasant to watch at all.

RACHAEL BROWN: Deakin University koala expert, Dr Desley Whisson, was part of the team.

She disputes the term cull and suggestions it was done in secret to avoid backlash from the community and green groups.

DESLEY WHISSON: It was totally about euthanising very sick koalas that had no chance of survival.

I'd prefer to call it a "welfare intervention".

And secondly it wasn't done in secret, it was done in a public place, there were plenty of people who observed what was happening.

RACHAEL BROWN: The program was conducted in consultation with Zoos Victoria and the Bureau of Animal Welfare.

DESLEY WHISSON: Koalas were caught and most of the times they were just picked up off the ground because they had no strength left to climb trees.

They were taken to a vet station, the vets anesthetised them, did a complete health check, and any koalas that didn't meet a criteria were euthanised.

RACHAEL BROWN: Now I understand the sustainability rate for koalas is about one per hectare, but what are we looking at at Cape Otway?

DESLEY WHISSON: Well in November 2013 in one of the blocks where I have been doing monitoring there were 23 koalas per hectare, but saying that 23 koalas per hectare, it might be 23 koalas sitting in about three trees that still have some leaf on.

Very high density and just not sustainable at all.

RACHAEL BROWN: The Environment Minister Lisa Neville isn't ruling out further culls but she's promising a more transparent approach in future.

LISA NEVILLE: What I can assure the community is that I'm getting the advice from the experts and whatever action it is that we decide we need to take for these koalas, I will be open and transparent with the community about it, they won't need to read about it years later in the paper.

RACHAEL BROWN: This is scoffed at by the Koala Foundation, which says its suggestions, to both sides of politics, have been ignored for 30 years.

Its CEO Deborah Tabart says the Cape Otway cull was illegal.

DEBORAH TABART: Since 1996, every senior minister for the environment has said that Australia will never cull koalas and it is illegal.

RACHAEL BROWN: What about if they can maintain the argument that it was on a health basis, that they were starving and they would have died anyway?

DEBORAH TABART: Then why do it in secret?

RACHAEL BROWN: She goes further, claiming in mid-2012, the Victorian Government submitted an arbitrary over-inflated estimate of its koala population so the animal wouldn't be listed as "vulnerable to extinction".

DEBORAH TABART: The Australian Koala Foundation would want to ask Minister Hunt did his department sanction it because the koala was listed as a federally listed species in May of 2012.

And it is interesting to note that the Victorian Government pleaded with the Federal Government, please don't list the koalas in Victoria and when we were looking at the decline curves that they had to do to sort of not meet that requirement, they missed out by 1 per cent.

RACHAEL BROWN: Dr Whisson agrees culls are illegal but she repeats this was a euthanasia program for sick animals.

But Deborah Tabart says the Victorian Government has brought shame on the Australian people.

DEBORAH TABART: There was no habitat, no linked habitat. The Victorian Government hasn't planted one tree to solve this problem and here they go in kill koalas under the guise of welfare.

It's appalling! This is a national icon that brings in $3 billion worth of tourist dollars. I just can't wait to get on my Twitter-sphere and ask the people of the world, you tell Australia how ashamed they should be for not taking care of this incredible species.

ELEANOR HALL: That's Deborah Tabart from the Koala Foundation, ending that report from Rachael Brown.