Repetition suppression (RS) is a reduction of neural response that is often observed when stimuli are presented more than once. Many functional magnetic resonance imaging (fMRI) studies have exploited RS to probe the sensitivity of cortical regions to variations in different stimulus dimensions; however, the neural mechanisms underlying fMRI-RS are not fully understood. Here we test the hypothesis that long-interval (between-trial) and short-interval (within-trial) RS effects are caused by distinct and independent neural mechanisms. Subjects were scanned while viewing visual scenes that were repeated over both long and short intervals. Within the parahippocampal place area (PPA) and other brain regions, suppression effects relating to both long- and short-interval repetition were observed. Critically, two sources of evidence indicated that these effects were engendered by different underlying mechanisms. First, long- and short-interval RS effects were entirely non-interactive even though they were measured within the same set of trials during which subjects performed a constant behavioral task, thus fulfilling the formal requirements for a process dissociation. Second, long- and short-interval RS were differentially sensitive to viewpoint: short-interval RS was only significant when scenes were repeated from the same viewpoint while long-interval RS less viewpoint-dependent. Taken together, these results indicate that long- and short-interval fMRI-RS are mediated by different neural mechanisms that independently modulate the overall fMRI signal. These findings have important implications for understanding the results of studies that use fMRI-RS to explore representational spaces.