The General Affairs Department is responsible for the basic day-to-day running of the foundation. This department handles such things as reception, information services, budgeting, and the settlement of accounts.

The Management and Planning Department handles such issues within the foundation as human resources development, and the planning of the foundation's general direction.

The Public Relations Department disseminates information about projects supported by The Nippon Foundation to the broadest possible section of society. It distributes information through such vehicles as newspaper and magazine advertisements, its website, and timely news releases.

The Maritime Affairs Department supports research projects dealing with the sea, in both the foreign and domestic spheres, financial support of the ship building industry, human resources development, and general maritime education programs.

The Domestic Program Department works with other Japanese non-profit organizations and community-based organizations to develop programs that build a better society. Examples include: self-sufficiency programs for those with disabilities, the donation of wheelchair-friendly vehicles, the protection of the environment, disaster relief programs and sports for people of all ages.

The International Program Department works for the betterment of people's lives, with a special focus on developing countries. It is particularly active in the areas of human resources development and the fulfillment of such basic human needs as hunger alleviation, public health and help for the disabled.

The Program Evaluation Department deals with the evaluation and auditing of existing programs.