The origins of Nippon Kaiji Kyokai date from the foundation in November 1899 of the Teikoku Kaiji Kyokai (the Imperial Marine Association) in Tokyo, which was established in order to promote the regulation and development of the shipping and shipbuilding industries in Japan. The early years of the Society were spent promoting a wide range of shipping-related activities, very different from the focused technical role that ClassNK plays today.

The first ship to receive a class certificate from the then TKK was the Kwanan Maru in 1920. In 1926, the Society's class notation, NS*, was formally registered in the classification clause of the Institute of London Underwriters, amounting to recognition of TKK's existence as an internationally active classification society. In the inter-war years, TKK recieved support from, and co-operated with, the British Corporation Register of Shipping (later to merge with Lloyd's Register) and other societies. By 1929, the Society had reached 1 million gross tons of ships under class.

The Society was relaunched under its current name, Nippon Kaiji Kyokai(the Japan Marine Association), in 1946 in the aftermath of World War Two.From a state of near complete destruction, the Japanese Shipping and Shipbuilding industries recovered gradually and then grew rapidly in strength, with the Society called upon to survey a large number and wide range of different vessel types over the years. The Society's Register of Ships had exceeded 10 million gross tons by 1966, and 100 million gross tons by the end of 1997. As of the end of 2008, Nippon Kaiji Kyokai has more than 7,000 vessels totalling over 160 million gross tons under class.

Reflecting the internationalization of both the shipping industry and the Society itself, a significant percentage of today's NK-classed ships are controlled by non-Japanese companies and shipowners, supported by a growing network of exclusive survey offices across the world and a system of national and technical committees. Following the establishment of offices in London and New York in 1962, the Society spread rapidly and now has exclusive survey offices in more than 70 locations, and representation in all major ports.

Nippon Kaiji Kyokai was a founding member of IACS, the International Association of Classification Societies, which was established in 1968 to represent the major national class societies and promote international initiatives and cooperation on ship safety. The Society has thrice held the Chairmanship of IACS, and is going to hold the fourth Chairmanship from July 2010.

Nippon Kaiji Kyokai celebrated its 110th anniversary on 15 November 2009. On 1 April 2011, the Society underwent a change in its organization, becoming a general incorporated foundation under Japanese law.

Just as in its earliest days, however, Nippon Kaiji Kyokai today remains an impartial third party, not-for-profit foundation, committed to promoting the safety of life and property at sea, and the prevention of marine pollution.