Authorisation would only be issued where the Department of Conservation was satisfied it will be safe for workers and the public, and minimised environmental impacts.
But Dr Margaret Stanley, an ecology senior lecturer at the University of Auckland, said while it may seem sensible to allow removal of dead trees, they were a "vital" part of the forest ecosystem.
There was a rich biodiversity of species that lived only on forest deadwood and decaying wood in turn acted as a "slow release" fertiliser - the main source of nutrients for new seedlings.
Many native species, from microbes and bacteria to fungi, lichens, reptiles, bats and birds rely on decaying wood on the forest floor.
"Kiwi and many other species eat insects that rely on decaying wood and vegetation so everything is interlinked in a forest ecosystem and removal of windblown trees will affect those linkages and inhibit forest growth," she said.
There was also a significant knowledge gap about the biological importance of decaying wood to native species which in turn has implications for biodiversity, she said.
"Less than half of New Zealand's approximately 70,000 native species have been scientifically described so there is a question over whether we actually know what we might be losing if we continue to degrade native forest."
Removing logs could further degrade forests by inadvertently damaging healthy trees as well as increasing the likelihood of disease and weed seeds being introduced by heavy equipment.
Dead tree removal was also likely to target larger trees which contribute the most to biodiversity.
Dr Stanley added while Dr Smith's proposed law change would focus on the effects of Cyclone Ita, it would also set a precedent for removing dead wood on conservation land.
While the minister had assured New Zealanders that no removal would take place within national parks, much of the area proposed for windblown logging is of high conservation value but had not been formally assessed for protection and so remained as "stewardship land", she said.
In a letter to the Herald, Sir Alan Mark, Emeritus professor of the University of Otago's Department of Botany, argued the forests that that had been formally protected should be allowed to undergo their natural replacement.
"Salvage logging by either helicopter or ground-based equipment, as the Conservation Minister proposes for substantial areas, would not only create further disturbance, but would also remove the very basis on which the new forest cycle depends - numerous sites with higher nutrients and light levels than the generally depleted (leached) soils on the much darker forest floor," Sir Alan said.
Canopy collapse released large amounts of nutrients into the ecosystem as the trees started to decompose, which was capitalised by birds and insects, as well as tree seedlings, he said.
"Preserving and understanding natural processes, no matter how destructive, is a key reason why we have preserved these conservation forests."
Under the bill, the recovery of timber was limited until July 1, 2019, when it expired, and all revenue from royalties would go to the Department of Conservation.
Dr Smith has said that allowing access to the wrecked trees would mean jobs for the West Coast and cash for the Department of Conservation for investment in other projects.
