A logging company owned by the Victorian Government may have broken the law during the controversial clearing of forest that's home to a threatened species, according to a formal complaint.

Key points: Conservationists allege logging in one East Gippsland experimental area was done so intensively, it may have breached the law

Conservationists allege logging in one East Gippsland experimental area was done so intensively, it may have breached the law Official complaint lodged with Environment Department

Official complaint lodged with Environment Department VicForests denies it breached any laws with its clearing

On Sunday, the ABC revealed VicForests was conducting an experiment in which it logs the habitat of the threatened greater glider using different techniques, and then measures how many gliders survive.

The logging company, which is fully owned by the State Government, has dubbed the experiment the "Greater Glider Project".

Greater gliders are listed as a threatened species under federal and state law.

At least a third of their population has been lost in the past two decades, with habitat loss listed as a threat with "catastrophic" consequences.

Conservationists have now alleged that logging in one of the experimental areas was done so intensively, it may have breached the law.

Ed Hill from the Goongerah Environment Centre has lodged an official complaint with the Environment Department and asked it to investigate.

"The Environment Department should throw the book at VicForests," Mr Hill said.

Professor David Lindenmayer, who is an expert on greater gliders, has described the experiment as "the terrestrial equivalent of so-called scientific whaling".

He said if the law had been breached, it would undermine the results that the experiment may produce.

"It would mean that they've actually messed up the treatments," he said.

VicForests has denied it breached any laws with its clearing, arguing Mr Hill has misinterpreted the requirements.

How does the logging experiment work?

Greater gliders are listed as a threatened species under federal and state law. ( Supplied: Jasmine Zeleny )

VicForests is required to maintain at least four "habitat trees" per hectare when logging forests in East Gippsland.

In one area where surveys revealed a high density of greater gliders before the trees were cut down, VicForests appears to have not left the required number of trees, Mr Hill said.

The official VicForests "retention map" identifies fewer than four trees were marked for retention per hectare over the entire area, according to the complaint.

And in at least one part of it, there was only one habitat tree marked for retention in a one hectare area.

Additionally, the conservationists argue at least one of the trees retained was too small and immature to qualify as a "habitat tree" — and so itself represents a potential breach of the law.

"The area within the experiment where very few trees have been retained is the same area that VicForests found greater gliders," Mr Hill said.

"They logged their entire home range areas, which has killed those animals."

VicForests said the requirement that it leave at least four trees per hectare was supposed to be averaged over the whole area.

A spokeswoman said since it left an area in the corner of the coup unlogged, the required average number of trees per hectare was met.

She also said small trees were allowed to be used as habitat trees when mature trees were not available.

When the ABC visited the site recently, there were stumps of very large trees that had been cut down, as well as large old trees pushed over and left on the ground.

Conservationists and scientists have criticised the VicForests experiment. ( ABC News: Michael Slezak )

VicForests said the experiment was attempting to find a balance between conservation of threatened species and the native forest logging industry, but acknowledged the logging was likely to kill greater gliders.

The area subject to the formal complaint is intended to be logged using "standard retention".

In VicForest's experiment, it is comparing that with a type of logging where they leave more trees — and seeing if that leaves more greater gliders.

Professor Lindenmayer said if the area was logged more intensively than standard retention allows, then that undermined the study's aims.

Victoria's Department of Environment confirmed to the ABC it had received the complaint, and said all reports of non-compliance were investigated.