The waters off Otago are home to some of the world's rarest species such as the New Zealand sea lion, royal albatross and yellow-eyed penguin, however their habitats remain at risk.
The government announced today a new plan for marine protection, an area equivalent to the size of Auckland.
"We actually protect very very little of our coastline and our species, yet we go out to the world with a clean green 100% pure brand, well this is part of delivering on that global promise we make." Fisheries Minister Stuart Nash told 1 NEWS.
The plan is designed to conserve habitats of at-risk species and is said to stretch from Timaru to the south of Dunedin.
There are concerns that it will impact commercial fishing as zones will be set in place.
Red zones will be marine reserves where fishing will be banned, and in the blue zones only some fishing will be allowed.
The country's fishing industry body supports protecting the environment but is skeptical about the method.
The restrictions are expected to cost the fishing industry 3.2 million dollars a year.
"We are keen to hear from people who fish in this area, but I do not accept that we are taking away quota or stopping people from making a living out of fishing." Mr Nash said.
Iwi representative Edward Ellison said it was a difficult decision that had to be made.