After prolonged exposure to moving stimuli, illusory motion is perceived in stimuli that do not contain consistent motion, a phenomenon termed the motion aftereffect (MAE). In this study, we tested MAEs under binocular suppression that renders the motion adaptor invisible for the entire adaptation period. We developed a variant of the continuous flash suppression method to reliably suppress target motion stimuli for durations longer than several tens of seconds. Here, we ask whether motion systems are functional in the absence of perception by measuring the MAE, a question difficult to address using binocular rivalry that accompanies a switch of percept between visible and invisible. Results show that both the MAEs with static and dynamic tests are attenuated with an invisible adaptor when the adaptor and the test stimulus are presented to the same eye. In contrast, when the test pattern was presented to the other eye, the dynamic MAE was observed in invisible adaptor conditions. These results indicate that low-level adaptation survives under total binocular suppression, a finding predicted by previous studies. In contrast, disappearance of interocular transfer in the dynamic MAE suggests that a high-level motion detector does not operate when the motion adaptor is rendered invisible.