The Vessels Intentions register is a joint effort between Environment Southland and Biosecurity New Zealand.
It provides a way for boat owners and operators to notify their intention of travelling to Fiordland, and enables the council and biosecurity officials to monitor their movements in the "most sensitive" of marine environments.
Environment Southland compliance manager Mark Hunter said the register would allow timely biosecurity information to be passed on and checks to ensure boats had thorough hull maintenance and antifouling coatings.
"Dirty boats spread marine pests, so regular cleaning and antifouling are vitally important.
"Introduced pests, such as the seaweed undaria, or the sea squirt Styela clava will readily hitch a ride on the hull of any moored vessel, particularly if it has a dirty surface to take hold on.
"Fiordland is precious and many parts are simply unique, so there's a lot at risk," he says.
The Southland regional pest management strategy and coastal plan outlawed travelling into the fiords with a fouled hull or discharging ballast within the fiords.
Hunter says the Vessels Intentions register was a voluntary measure.
Details would be kept in confidence by Environment Southland and Biosecurity New Zealand (a division of the Ministry of Agriculture and Forestry).
Boat users could access the register to log their intended here.
The vessels intentions register was a part of the effort to enact the Fiordland Marine Conservation Strategy.
Read more about antifouling here.