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The National Museum  started in 1901 as the Insular Museum of Ethnology, Natural History and Commerce under the Department o f Public Instruction by virtue of Act No. 284 passed by the Philippine Commission. The name was changed in 1903 to Bureau of Ethnological Survey under the Department of  Interior. After the St. Louis Exposition in 1904 the Office was renamed the Philippine Museum. The Bureau of  Ethnological Survey which had a division called the Philippine Museum was abolished as a separate bureau and was made merely a Division of  Ethnology under the Bureau of Education by virtue of Act No. 1407. In 1906, the Philippine Commission transferred the Division of  Ethnology of the Bureau of Education to the Bureau of Science which had other branches of Natural Science such as botany, geology and paleontology, entomology, ichthyology, herpetology and mammalogy. 

In 1916, the Philippine Legislature passed Act No. 2572 organizing the Philippine Library and Museum from the former division of archives, patents, copyright, trademarks and corporation of the executive bureaus; the former law library of the Philippine Assembly and the former Philipine Library. The Division of Ethnology continued to function under the Bureau of Science. In 1926, Act No. 3437 passed by the Philippine Legislature recreated the National Museum of the Philippines as part of the Department of Agriculture and National Resources and these consisted of the Ethnology Division and the Division of History and Fine Arts. The Division of Natural Science was not included in the organization. 

 Again in 1933, the Philippine Legislature passed Act No. 4007 abolishing the National Museum and distributing its activities, functions and materials to the following: 

1. The Division of Fine Arts and History  to the National Library; 
2. The Ethnology Division to remain with the Bureau of Science; 
3. The Division of Anthropology which included archaeology, ethnography and physical anthropology and the other sections of natural history of the Bureau of Science were organized into a National Museum Division with Dr. Leopoldo B. Faustino as its first chief.
In 1939, an administrative order  renamed the division as the Natural History Museum Division, but after the Commonwealth Act No. 453 made the Division an independent unit directly under the office of the Secretary of Agriculture and Commerce. 

The Japanese occupation saw the abolition of the Natural History Museum Division, but after the liberation of the Philippines in 1945, it was reestablished under the Department of Agriculture and Commerce and placed it under the Office of the Executive Secretary. In 1951, Executive Order No. 392 transferred the National Museum to the Department of Education.

Old Congress Bldg after World War II
The reorganization of the Department was implemented in 1988. The National Museum's organizational structure together with its functions were improved and expanded. The Archaeology Division was created from a section of the Anthropology Division. It's function is to conduct researches on the prehistory of the Philippines in order to define the foundation of the culture of the people through systematic archaelogical excavations of land and underwater sites. Two existing divisions were renamed and their functions were expanded: the Restoration and Engineering Division takes charge of the implementation of Presidential Decree Nos. 260 and 756. It conducts nationwide surveys and documentation of important immovable cultural properties of the Philippines and has general  supervision  over the restoration, preservation,, reconstruction and remodelling of immovable cultural properties. The Archaeological Sites and Branch Museum Divisions that administers. maintains, preserves artifacts in situ in the archaeological sites, is also authorized to establish branch museums in the different regions of the country, concomittant with its goal of bringing the museum closer to the majority of the people in the countryside. 

In  the same year, two Presidential Proclamations on culture were issued by the President of the Philippines, pursuant to the 1987 Constitution, giving priority programs to the arts and culture. These were Presidential Proclamation No. 269, proclaiming the period from 1988 to 1998 as "The Decade  of  Centennials of the Filipino Nationalism, Nationhood and the Philippine Revolutionary Movement" and Presidential Proclamation No. 270 authorizing the National Museum to conduct a National Educational and Fund Campaign for the period June 12, 1988 to June 12, 1989. 
    On 26 January 1996, President Fidel V. Ramos signed Administrative Order No. 246 that created a Presidential Committee to oversee the rehabilitation of the National Museum complex. Earlier in October 1994, the President instructed the Secretaries of Finance and Tourism to prepare for the eventual turnover of the Finance and Tourism buildings to the National Museum.
In December 1995, the Department of Finance transferred to Bangko Sentral Complex and turned over the Finance building to the National Museum.  The Department of Tourism was scheduled to turn over the Tourism building by the end of 1997.

In mid-1996, the Philippine Senate, in a historic move, vacated the Senate Chambers of the Executive House paving the way for its turn over to the National Museum thus providing the institution with the three buildings within the Agrifina Circle that would now form the National Museum precinct, the heart and soul of the National Museum system.

On February 12, 1998, President Fidel V. Ramos approved and signed Republic Act No. 8492, also known as the 'National Museum Act of 1998' that established a National Museum System and provided for its permanent home, among others. 

In June 1998, the new National Museum located at the former Finance Building precinct was opened with the formal  inauguration of the National Museum of the Filipino People and the exhibition of the permanent exhibit, The Story of the Filipino People, and the world-class travelling exhibit,  The Treasures of the San Diego,  which was returned to the Philippines after its world tour of Paris, Madrid, New York and Berlin.  The formal inauguration formed a key part of the grand celebration of the Philippine centennial. 


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