A new method to analyze transformation processes of work procedures for on-site workers engaged in organizational activities, based on the concept of the four levels of contradictions, is proposed. Various contradictions, i.e., misfits between components of the activity system, might arise out of and propagate throughout their activities, then induce some sorts of changes in the procedures for the better or for the worse. The proposed method, focusing on the negative aspects of such procedure transformation, represents every phase of a changing activity in terms of a diagrammatic triangle of Engestrom’s activity theory, thereby visualizing the process of its changing with latent contradictions can contribute to the in-depth analysis of organizational accidents. Within organizations, a human plays variable roles as an agent that is an actor, an observer, a cognizer, and an interpreter, which produces a complex organizational behavior. In order to model this, we introduce the subject of C. S. Peirce’s semiosis, which is any form of activity, conduct, or process that involves signs, including the production of meanings. The criticality accident occurred at the nuclear fuel conversion facility of JCO (1999) is employed for an illustrative case to explain this method’s capabilities.