In an earlier study, we demonstrated that the temporal rate adaptation effect can be transferred from audition to vision and vice versa. However, it was unclear whether this effect was due to a top-down cognitive process, or rather to an earlier calibration process which is stimulus-driven and automatic. We therefore examined the effect of interocular masking of the adapting stimuli on the temporal rate adaptation and its cross-modal transfer from vision to audition (VA). Participants were trained, using feedback, to classify repetitive auditory stimuli presented at a range of frequencies (3.25–4.75 Hz) as fast or slow (as compared to the average frequency of 4 Hz). Afterwards, subjects were repeatedly exposed to visual stimuli at a specific rate (3 or 5 Hz). This adaptation stimulus was masked by continuous flash suppression (CFS). During CFS, a stimulus presented to one eye can be suppressed from awareness by a stream of constantly changing images in the other eye. To test whether adaptation resulted from this less visible exposure, participants then performed the same task as in the training, but without feedback. Test and adaptation tasks were presented in 20 alternating blocks. A comparison of the pre- and post-adaptation responses showed cross-modal changes in subjects’ perception of temporal rate. Adaptation to the masked 5 Hz (3 Hz) stimuli led to subsequent stimuli seeming slower (faster) than they had before adaptation. Since the adaptation stimuli were mostly masked by CFS, the results suggest that temporal rate adaptation and its cross-modal transfer occur mostly at a subconscious level.