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As well as finding cures for diseases, the project also aims to explore new markets for TCM.
Shang expressed the wish that "the project can promote the market share of traditional medicines in the global healthcare business."
It will also adhere to the government's previous vow that companies should play the major role in innovation, by promoting the establishment of first-class joint clinical centres and laboratories.
The ministry said the list of the 50 programmes was still being finalized. "Basic criteria include outstanding effectiveness and use of technology," the official said.
The project also includes training for professional TCM doctors and researchers, and advocacy of knowledge about traditional medicine.
An international office is also planned to co-ordinate the project, which is expected to attract both government and business leaders.
World Health Organization statistics show that 75 countries have established natural medicine administrations. And 51 countries have laid out policies to develop indigenous traditional medicines.
Acupuncture is legally accepted in a number of countries, and the export of TCMs has witnessed a steady growth in recent five years.
However TCM is a contentious issue in some places due to a lack of understanding and shortage of new products.