The General Meeting is formed by regular JPNIC members who agree on its activities. In the General Meeting, important matters relating to the administration of JPNIC are resolved, budgets and account settlements are resolved and approved, and Trustees and Auditors are selected.

The Board of Trustees and the Executive Board administer the organization of JPNIC and approve policies and rules resolved by the General Meeting. Important policies are referred to discussion by the Committees organized by external experts, reviewed by the Policy Advisory Council, the function of mutual coordination, then advanced to the Board of Trustees.

JPNIC's operations are shared by the IP Address Department, Domain Name Department, Internet Development Department, Engineering Department, and Administration Department under the direction of the Secretary-General.