Japanese officials said that the government would respect the court's decision. But the ruling related specifically to Japan's hunting of around 900 minke and fin whales for scientific purposes - known as Jarpa II - and its government could reapply for a different permit.
It could also decide to break away from the International Whaling Commission (IWC). Iceland and Norway continued to defy the commission by hunting whales commercially.
Mr McCully said it was a promising sign that Japan had confirmed it would remain as an IWC member. He was confident that the judgement would make it difficult for the country to resume whaling in waters south of New Zealand.
Watch: Court stops Japanese whaling ships
It could also form the precedent for preventing whaling in other regions, such as the northern Pacific Ocean, where Japan catches a smaller number of whales.
Green Party oceans spokesman Gareth Hughes said New Zealand needed to continue diplomatic pressure on Japan to make sure it did not exploit any legal loopholes.