The Tokyo National Research Institute for Cultural Properties was originally founded in 1930 as The Institute of Art Research with an endowment bequeathed by KURODA Seiki. It was then reorganized in 1952 into the Tokyo National Research Institute of Cultural Properties with the establishment of Departments of Fine Arts, Performing Arts, and Conservation Science, and the Section of General Affairs. The Department of Restoration Techniques and that of Archives were added in 1973 and 1974, respectively. The Japan Center for International Cooperation in Conservation was established in 1955.
From April 2001, the Institute was renamed the National Research Institute for Cultural Properties, Tokyo and started its new history as a branch of the Independent Administrative Institution with some changes to the former organization. The Department of Archives was abolished and the Chief Coordination Manager – Archives Section was newly established. The former Division of General Affairs (originally, the Section of General Affairs) became the Department of Management.
In April 2006, the organization of the Institute was restructured again: the Chief Coordination Manager – Archives Section was changed into the Department of Research Programming and the Department of Performing Arts into the Department of Intangible Cultural Heritage.
In April 2007, the Institute became a branch of the Independent Administrative Institution, National Institutes for Cultural Heritage. The Department of Fine Arts was incorporated into the Department of Research Programming, and the Department of Conservation Science and that of Restoration Techniques were integrated to form the Center for Conservation Science and Restoration Techniques.
In April 2010, the Department of Management was renamed the Department of Research Support and Promotion.
In April 2011, the Department of Research Programming was renamed the Department of Art Research, Archives and Information Systems.
In April 2016, the Center for Conservation Science and Restoration Techniques was renamed Center for Conservation Science.