In 1955, Watkinson was appointed Chief of Occupational Health by Paul Martin, Minister of Health and father of Paul Martin (Jr.), who served as Prime Minister of Canada from 2003 to 2006. During his tenure he presided over the thalidomide crisis and was instrumental in awakening Canadians to the dangers of smoking cigarettes. More and more of Watkinson's professional time was taken over by dealing with the effects of atomic radiation. Colleagues of Watkinson's included Sir John Cockcroft, Candau (Director of the World Health Organization), Cipriani, and W. Lewis.