日本於1998年制定《中央政府等改革基本法》，並以之作為推動獨立行政法人之指導方針。2001年4月，東京國立博物館在政府的強制執行下，從文化廳管轄下的機構轉型成獨立營運的博物館。之後，奈良、京都和九州3座國立博物館亦相繼轉型，並與東京國立博物館共同組成一個「獨立行政法人國立博物館」的組織體，進而於2007年4月與獨立行政法人文化財研究所整併為「獨立行政法人國立文化財機構」。從此，東京國立博物館變成「獨立行政法人國立文化財機構‧東京國立博物館」，在營運管理上最大的不同在於：（一）須擬訂中期計畫及年度計畫，並須經過文部科學省及總務省評鑑，評鑑結果不佳者，須重新檢討，甚至被勒令停止營運。（二）原來屬於國有的文化遺產、建物及土地等都移轉為獨立行政法人國立博物館所有。（三）其營運所需經費由政府的「營運費交付金」提撥預算，在預算執行上具有高度變通性，但卻有自籌經費目標不斷增加以及盈餘運用之設限等問題。 讓業務具有計畫性、公開性及透明性，是獨立行政法人化所帶來的正面效果，但在政府諸多限制下，轉型後的國立博物館營運仍面臨諸多窘境。筆者認為除了所有產權應該維持政府所有之外，政府必須做到下列幾點，獨立行政法人才有充分發展的可能性，包括：（一）營運預算不得統一刪減；（二）增加博物館預算運用的自由度；（三）允許博物館活用剩餘款；（四）不設定收益業績；（五）確保不受省廳管轄的獨立性；以及（六）維持足夠的館務人員。

In April 2001 Tokyo National Museum was coerced by the government to transform from an institute subordinate to the Agency for Cultural Affairs into an independent administrative institution according to“The Basic Laws of Reform for Central Government, 1998”. Then three other national museums in Nara, Kyoto and Kyushu followed, and these three and Tokyo National Museum were joined together as an organizational entity of“Independent Administrative Institution National Museum.”It was further arranged before long and named“Independent Administrative Institution, National Institute for Cultural Property” when it was merged with the“Independent Administrative Institution Research Institute of Cultural Properties”in April, 2007. The Tokyo National Museum was thus with the new title of“The Tokyo National Museum of the Independent Administrative Institution National Institute for Cultural Property”, and it has three major differences in operation management comparing with what in usual: (1) Medium and long-term plans as well as annual plans should be submitted for approval, and evaluation to be conducted both by Ministry of Education, Culture, Sports, Science and Technology and by Ministry of Internal Affairs and Communications. If the evaluation outcome was not well enough, the museum was required either to make self-examination or to be forced to end its operation. (2)The formerly government-owned cultural heritage, buildings and land were transferred to the Independent Administrative Institution National Museum. (3)The budget for operation was allotted from the government in the name of“Grant for operating expenses”with more flexible in budget implementation, however, the increase of the ratio of self-financing and the restriction on the use of surplus all caused problems. The positive effect of operating the independent administrative institution showed in a more planned, open and transparent practice. Due to a good deal of restriction from government, the operation of those transformed national museums were in awkward circumstances. If such independent administrative institution is to be fully developed, I think, the government should remain the ownership of national properties, and meanwhile put following points into practice: (1) not to treat all museums alike by cutting operating budget equally; (2)to give each museum more freedom in budget expending; (3) to allow a museum to use its annual balance flexibly; (4)not to stipulate the business income as required; (5)to keep the museums operate independently without being governed by ministries or agencies; and (6)to keep enough staff to run a museum properly.