Several disease presentations are linked to a mismatch between the real body and the body’s internal representation of itself. In order to develop effective rehabilitation therapies, it is necessary to understand the mechanisms underlying changes in body representation. In this study, we focused on changes in body representation of the upper limb as a large part of the body and investigated the conditions under which such changes occur. Participants were presented four conditions which differentially affected their sense of ownership and agency, including a movement condition related to their sense of agency, and a visual hand information condition related to the sense of ownership. In the experiment, participants were asked to move their upper limb forward and backward on a manipulandum. Results of the study showed that visual hand position affected changes in body representation relevant to both conscious and unconscious body parts. In addition, changes in the representation of the unconscious body part occurred with, and were dependent on, active movement.