In 1962, Watkinson was appointed Assistant Director of the Health Services Branch of the Health Department of Canada. Watkinson's health duties included being constantly aware of new hazards to the public health. Watkinson's gave his attention to the possible effects of cigarette, pipe and cigar smoking on the health of Canadians. A study of the health of war veterans, made earlier by his Department, had shown a relationship among tobacco smokers with certain lung and heart diseases. Also, a well-known British epidemiologist, Doll, had just published a report on his studies of the effects of smoking on the health of smokers. On the basis of these investigations, Watkinson finally decided that it was necessary for a Canadian program to counter the effects of tobacco smoking. Watkinson was a pioneer in educating Canadians to the dangers of smoking through a new national campaign. He also called the presidents of all of the major Canadian tobacco companies to Ottawa to discuss the issue and encouraged Tobacco farmers to search for another suitable crop.