Tôn Thất Tùng played an important role in investigating suspected use of germ warfare during the First Indochina War. Even though he was trained as a surgeon, his role in the medical corps and ministry of health of the Việt Minh meant that he took on such responsibilities.

In addition to serving as the chair of the first meeting of the Committee to Prevent Germs (Ban Chống Trùng or BCT), he served as the president of the planning group assembled after the third meeting of the BCT. Among other things, this group laid out three guiding principles to deal with biological weapons. These were:

1. The response to natural disasters should be used as a basis for the response to combatting enemy-inflicted destruction;
2. The Masses (i.e. the People) should be the basis of response;
3. There are two kinds of hygiene: short-term campaigns and everyday, regular practices. The short term campaigns are useful to establish regular practices and the regular practices are a continuation of limited-time campaigns.

This alleged use of biological warfare in the early 1950s by the Americans and French in Korea and Vietnam helped frame the subsequent use of chemical herbicides, including Agent Orange, by the American and South Vietnamese militaries from 1961 to 1970. By that time Tùng had largely stopped his surgery practice but he continued an active research program into the possible effects of herbicides on present and future generations of North Vietnamese.