Documents released under Freedom of Information laws have revealed Forestry Tasmania was advised not to log part of a coupe on South Bruny Island because of its potential as a swift parrot habitat.
The report by the state government's Threatened Species Section says the coupe should be reserved for the endangered bird.
Forestry Tasmania has admitted to logging half the coupe and says more is planned.
It says it received subsequent verbal advice from the Threatened Species Section saying it was all right to harvest the area.
The Greens have described it as environmental vandalism, but Ken Jeffreys from Forestry Tasmania says the criticism ignores the bigger picture.
"It would be an absolute cheap shot if you focused on one coupe, one small area of Tasmania and ignored the amount of work that Forestry Tasmania's put into the swift parrot habitat across the landscape," Mr Jeffreys said.
The Greens' Cassy O'Connor says the state and federal governments need to stop the logging.
"That is the most ridiculous argument. Every piece of habitat counts for a species that is down to 1000 breeding pairs," Ms O'Connor said.
"So, when you hack down coupes that are important for the species, you impact on their survival," she said.