The NDL belongs to the National Diet and is supervised by the Speaker of the House of Representatives and the President of the House of Councillors or more specifically by the Standing Committees on Rules and Administration of the two Houses. The presiding officers of the two Houses appoint the Librarian of the NDL with the approval of the Houses, and the Standing Committees on Rules and Administration examine and approve NDL's management rules, operations and budget. As of April 2010, the Library has 890 staff including the Librarian and Deputy Librarian. Regular staff are recruited through open competitive examinations.

• The NDL consists of following libraries:
  • (1) The Main Library comprising the Administrative Department, Research and Legislative Reference Bureau, Acquisitions and Bibliography Department, Public Services Department, Reference and Special Collections Department, and the Kansai-kan.
  • (2) The International Library of Children's Literature
  • (3) Twenty-seven branch libraries in the executive and judicial agencies of the government

The Branch Libraries in the government ministries, agencies and the Supreme Court not only provide library services but also acquire government publications for the NDL. This unique function of Branch Library System has no counterpart in other countries.

*Link to the Organization Chart of the National Diet Library

On March 31, 2009 the branch library agreement between the Toyo Bunko (Oriental Library) and the National Diet Library was canceled. The Toyo Bunko continues its reader services.