Wildlife officials did three euthanasia sweeps to kill 686 koalas in 2013 and 2014, in a covert campaign that was designed to avoid any backlash from green groups and the community.

The secret cull was conducted under the previous Liberal government near the Great Ocean Road to address overpopulation issues.

The marsupials were starving due to overpopulation in the Cape region, which is said to have the greatest density of koalas in Australia.

The koalas were captured and sedated before being put down.

Koala expert Dr Desley Wisson, from Deakin University, told radio 3AW the cull was needed.

"Koalas had built up to quite high densities in manna gum areas down at Cape Otway," she said.

"It got to the point where there were no leaves left on the trees and the koalas were literally falling out of trees.

"They were dying of starvation."

Dr Wisson said the koalas had been introduced to the Cape manna gum areas.

"They absolutely adore manna gum ... so they tend to find those manna gum locations and just sit there," she said.

But it was difficult to relocate the koalas.

"It's actually not a very nice thing to move a koala; a lot of them will actually die [from stress] during that process." 

Environment Minister Lisa Neville told radio station 3AW no more culls would be done in secret.  She would put in place a special koala management program after seeking advice from experts.

"I don't want to see koalas suffer," Ms Neville said.

"I'm making sure the advice comes to me as quickly as we can and we will obviously be very open and transparent with the community.

"It is challenging, it is distressing ... but I think it's absolutely important that we are open with the community."

Frank Fotinas, who runs the Bimbi Park Caravan Park at Cape Otway, told ABC radio the area smelt of dead koalas.

"A lot more were dying naturally than were euthanased," he said.

"The whole of the Cape smelt of dead koalas.

"It smelt like death. You should come and look at the trees. There are hundreds of acres of dead trees."

The Australian Koala Foundation's CEO, Deborah Tabart OAM has written to Greg Hunt MP, Federal Minister for Environment, following the news that hundreds of Koalas have been secretly culled in Victoria. 

The Australian Government needs to be held accountable. The AKF is looking forward to Minister Hunt's response.

click here to read the email Ms Tabart sent to Mr Hunt.