Two destroyers with more than 500 crew on board sailed into Wellington harbour accompanied by the New Zealand navy ship HMNZS Canterbury.
The JS Ise and destroyer JS Suzunami were on an Indo-Pacific deployment and arrived from Sydney, where Japan's military took part this month in war games involving New Zealand, Australia and other countries.
The Wellington visit was a ceremonial one, but it came as Japan, whose only treaty ally is the United States, has increasingly sought to deepen bilateral military co-operation amid ongoing regional tensions.
"Our defence force are developing cooperative work, not only with New Zealand and Australia but also many Pacific Island countries," Japan's envoy to Wellington, Makoto Osawa, told reporters Friday. "Our main goal is the free and open Indo-Pacific."
The ambassador's remarks followed the announcement on Tuesday by Australia's government that Japanese firm Mitsubishi Heavy Industries had won the bid for a contract to build Australian warships, beating out a German firm.
While officials in Canberra said the Japanese proposal was the best and cheapest, they also hailed it as the biggest defence industry agreement between the countries.
New Zealand too has sought to shore up its strategic and military relations in Asia as part of a foreign policy reset in recent years that the government says has turned more attention on Pacific co-operation and security.
Officials in Wellington announced in July that work had started on a defence logistics agreement with Japan, intended to make it easier for the countries' militaries to work together.
Japanese naval vessels do not often make visits so far south in the Pacific Ocean, but the rich and strategically important waters of New Zealand, Australia and smaller Pacific Island countries are increasingly contested by the world's major powers, making it the site of a fierce battle for influence between Beijing and Western nations.
Although remote, New Zealand has recently been drawn into more fraught questions of regional security.
In February, live firing exercises by Chinese naval frigates in the Tasman Sea between New Zealand and Australia drew alarm from those countries' governments after flights were forced to divert at short notice.
The last port visit to Wellington by a Japanese naval vessel was in 1936, New Zealand's military said. A Japanese ship visited New Zealand's largest city Auckland in 2016.
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