While recent studies show dissociation between the implicit and explicit aspects of ‘sense of agency’, the mechanisms underlying these different aspects of agency are not yet clearly understood. We argue that the control achieved at different levels of hierarchy is important for different aspects of agency. In the current study, we investigate how changes in control at the perceptual-motor level and at goal level influence implicit and explicit measures of sense of agency. In a given trial, participants were first required to aim at a target in a noisy environment and then shoot at the target. After certain interval, a circle flashed at the location where participant aimed while pressing the trigger. Participants estimated the interval between action and presentation of the circle that acted as a measure of intentional binding, an implicit measure of agency and also rated an explicit sense of authorship. The results suggest that different aspects of agency and dissociation between implicit and explicit aspects of agency are mediated by control achieved at various levels.