In 1959 the Pension Bureau was created out from the Health Insurance Bureau within the Ministry of Health and Welfare. Later in 1962 the Social Insurance Agency was established to take over the operational business of social insurance schemes which these Bureaus used to be in charge of. The Agency is an external organization of the Ministry in charge of operation of social insurance scheme such as employees' health insurance and pension insurance.

In 1988 the Agency's organization was restructured in the aim of more efficient social insurance operation. As the result, the internal organization consisted of:

･General Affairs Department in charge of overall management of the Agency
･Administration Department in charge of administration of social insurance related businesses
･Social Insurance Operation Center which operates closed circuit on-line system to process social insurance related data, and
･Social Insurance Collage which provides the Agency's officials with expert training courses

In April 2000 the Social Insurance Bureau, national government organization was established in every prefecture. Their branch Social Insurance Offices, formerly prefectural government organization, also became national government organization. This reformation declared that the social insurance business such as contribution collection or benefits payment, is the responsibility of national government.