Conservation boards says the Department of Conservation has failed to explain how boards are supposed to work with the new regional boundaries.
The department plans to merge 11 conservancies into six.
At present there are 13 boards with up to 12 members each, set up under the law to provide community advice to the department.
They are responsible for creating long term plans to manage and protect the natural and historic features and wildlife of their region.
Otago Conservation Board chair Abby Smith says the reorganisation of DoC boundaries means the area her group administers will be split into two conservancies.
Professor Smith says DoC has not explained how how they will work under the new regime.
She says the changes may jeopardise her board's recent plans.
"We've just put together over the last couple of years a draft conservation management strategy for Otago.
"We don't know whether the conservation management strategy will apply to these new conservancy boundaries or whether they are meant to be abandoned, or completely redone."
She says South Island boards are also worried centralised managers won't understand the risks and unique features of remote parts of the new, larger conservancies
Conservation Minister Nick Smith says when the reorganisation is complete, he intends to review the number of conservation boards to see how they can be integrated with the new structure.