Foreign Affairs Minister Murray McCully said it was important that New Zealand played its part in the region as a member country of the Convention for the Conservation of Antarctic Marine Living Resources.
Lieutenant Commander Rob McCaw, the Otago's commanding officer, said his crew had been training for six months for the trip to the Southern Ocean, which he said was the "most inhospitable place on the face of the planet".
"Having deployed as Captain of the Otago to the Southern Ocean last summer season, I know what we have in store and I know how the team and I will be challenged - there is nothing I have done in my naval career to match it."
Ministry for Primary Industries officials were on board the Otago and would inspect the fishing fleet - which included three New Zealand boats - for compliance.
The Navy patrol remained in place until the agreed catch limits were reached, usually in January or early February.