The state government's timber agency has apologised for the death of a koala in one of its logging coupes, but has continued harvesting in an area that is home to the endangered Greater Glider.

As The Sunday Age revealed last week, the dead koala was found between logged trees in a forest in the Acheron Valley – a central highlands area the Andrews government could have protected, had it not ignored advice from its scientific committee.

After graphic images were published in the media, VicForests sent a letter to stakeholders admitting its procedures to protect the iconic native animal had failed, and "we deeply regret that this has happened".

"VicForests follows procedures in its timber harvesting operations for the protection of koalas and unfortunately these were not successful on this occasion," wrote acting chief executive Nathan Trushell.