"We're building all of these things, and we need to have renewable energy - but it has to be done in such a way to not make things worse for critically endangered species."
Dr Woehler was unable to quantify the bird deaths but said that anecdotally, as more wind farms were emerging, greater numbers of birds were being found dead with blade-strike injuries.
Last year alone, 29 wedge-tailed Eagles died after flying into overhead powerlines associated with Tasmanian wind farms, he added.
The island state already had three wind farms, but another 10 were in the works and the "most worrying" is the looming largest in the southern hemisphere on Robbins Island, in far northwest Tasmania.
"Its turbines will threaten migratory Arctic shorebirds, some already listed as critically endangered, that make the Robbins Passage-Boullanger Bay wetland complex their southern summer home," Dr Woehler said.
The island is used by migrating orange-bellied parrots and tens of thousands of other shorebirds.
Wetlands need to be crossed for construction on the island.
"It might be windy, but they are not looking at other environmental issues," he said.
Birdlife Tasmania is calling for a strategic approach to wind farms that takes in all environmental effects from both state and federal governments.