Scientists working to save a critically endangered species say they are shocked and frustrated about the logging of a known swift parrot nesting site in southern Tasmania.

Dr Dejan Stojanovic, a conservation biologist at the Australian National University, said he and his research team had been monitoring the habitat at Tyler's Hill for a decade.

Last week he visited the site to plan for the installation of predator-proof nest boxes, used to protect the birds from sugar gliders.

Upon arrival he found the area had been felled.

Researchers were "shocked" to find the coupe had been felled. ( Supplied: Dr Dejan Stojanovic )

"It was pretty shocking to be honest," Dr Stojanovic said.

"I went there with this really positive headspace of 'we're going to improve this habitat and make it a better place for swift parrots to breed'."

"On arrival this whole patch of bush where these birds had nested for over 10 years of our monitoring, just gone.

"It's really just a heartbreaking and frustrating experience, it makes you kind of wonder why are we doing this?"

The area is a registered logging coupe for Sustainable Timber Tasmania, formerly known as Forestry Tasmania.

In 2016 the government entity failed to achieve Forestry Stewardship Council (FSC) certification on a number of points, including threatened species management.

FSC advised the company it needed to, among other things, identify swift parrot nesting habitat before its forests could be labelled "environmentally, economically and socially responsible".

Dr Dejan Stojanovic holds a swift parrot ( Supplied: Dr Dejan Stojanovic )

"It's very disappointing as a conservation scientist to come to an area like this, to see that even those basic kind of conservation prescriptions are obviously not being applied on the ground," Dr Stojanovic said.

With just 2,000 birds left in the wild Dr Stojanovic said it was critical for the Tasmanian Government to ensure no more of their habitat is lost to logging.

"We're continually logging in new areas of swift parrot habitat, despite the fact that we know logging is the principle cause of the species' decline," he said.

"Protecting swift parrots is actually not that hard, it's just about not cutting down mature trees in areas where we know swift parrots need them."

Only about two thousand swift parrots survive in the wild. ( ABC News )

Swift parrots are migratory, spending autumn and winter in south-eastern Australia and travelling to Tasmania to breed during spring and summer.

"They need this habitat, we've just taken out a substantial area of their critical habitat at a critical time of year," Dr Stojanovic said.

Wilderness Society spokesman Vica Bayley said that by allowing the area to be logged the Tasmanian Government is undermining the species rescue effort.

"The swift parrot cannot afford the loss of more key nesting habitat and [the] Government must urgently step in," he said

"Where is this management plan? Environment Minister Elise Archer needs to step up and support this species by ending logging in all habitat areas before it is too late."

Conservationists accuse the State Government of undermining its threatened species rescue efforts. ( ABC Rural: Margot Foster )

In a statement, Ms Archer said "the Department continues to work closely with the Forest Practices Authority to ensure appropriate management of Swift parrot habitat".

"Ongoing discussions with Sustainable Timber Tasmania (STT) are aimed at developing a strategic landscape approach to the management of the species," she said.

"STT is working with Swift parrot researchers to develop this approach, and has indicated that this process may be completed by the end of 2017."

In a statement STT said no "identified and recorded nest trees" were harvested.

"Sustainable Timber Tasmania is committed to [the] protection of threatened species, and recognises that some swift parrot habitat coincides with some areas of public production forest," the statement read.