Physics learning situations often involve many cognitive conflicts between a student's present understandings and new information being learned. Cognitive conflict is known as an important factor in conceptual change. Therefore, it is important to help physics teachers and students develop skills and knowledge for more effective conflict management. However there is no readily available method to monitor the existence and features of cognitive conflicts that students may encounter during their learning. We focus the study on student anxiety caused by cognitive conflict so that we can improve student motivation. This study is targeted to develop an easy-to-use instrument that can be implemented in the classrooms to monitor student anxiety in cognitive conflict situations and the effects on student motivation. In this paper, we will discuss the structure of this instrument and show results from using this tool in our Physics by Inquiry class.