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The rescue and excavation of the Peinan Site brought about the planning and construction of the NMP.

In July 1980, while the construction of today's South Line Railway Station (formerly called the Peinan East Line Railway Station) and switchyard was in progress, the building work revealed prehistoric remains of great interest on the Peinan Site. Many slate coffins and exquisite artifacts buried with the dead inside the coffins were excavated one after another, and attracted great interest from the public, as well as unfortunately, some illegitimate excavation and looting due to extensive coverage from the media.

After Taitung County Government submitted a proposal to the relevant authorities, the construction of the railway station was halted. Furthermore, Professor Wen-hsun Sung of the National Taiwan University was delegated to recruit students and form the Peinan Culture Archaeology Team to carry out excavations and preservation.

Since then, for over 10 years, Professors Wen-hsun Sung and Chao-mei Lien have led the National Taiwan University Archaeology Team at the site during the summer/winter vacation periods. The area of excavation is over 10,000m2, and over 1,500 burials and tens of thousands of pieces of pottery and stone artifacts have been excavated. This area is definitely the biggest site in the archaeological history of Taiwan. Both scholars in Taiwan and from overseas agree that it is the most important and representative site of the mid-late Neolithic Age in Taiwan. The area is also the largest slate coffins burial complex with in the region of the Pan-Pacific Ocean and South-East Asia.

Professor Wen-hsun Sung has suggested that if we are to preserve the Peinan Site, an outdoor museum regarding the site should be built nearby. This was the first proposal for building a museum based on the Peinan Site. After all discussions and arguments, the NMP Planning Bureau was finally established on February 1, 1990. After 11 years of planning and construction, the NMP started its trial operation on July 10, 2001, and officially opened on August 17, 2002. It has established a foundation for the continuing development of the preservation and study of Taiwanese prehistoric culture.