The predictive coding model of perception proposes that successful representation of the perceptual world depends upon canceling out the discrepancy between prediction and sensory input (i.e., prediction error). Recent studies further suggest a distinction to be made between prediction error triggered by non-predicted stimuli of different prior precision (i.e., inverse variance). However, it is not fully understood how prediction error with different precision levels is minimized in the predictive process. Here, we conducted a magnetoencephalography (MEG) experiment which orthogonally manipulated prime-probe relation (for contextual precision) and stimulus repetition (for perceptual learning which decreases prediction error). We presented participants with cycles of tone quartets which consisted of three prime tones and one probe tone of randomly selected frequencies. Within each cycle, the three prime tones remained identical while the probe tones changed once at some point (e.g., from repetition of 123X to repetition of 123Y). Therefore, the repetition of probe tones can reveal the development of perceptual inferences in low and high precision contexts depending on their position within the cycle. We found that the two conditions resemble each other in terms of N1m modulation (as both were associated with N1m suppression) but differ in terms of N2m modulation. While repeated probe tones in low precision context did not exhibit any modulatory effect, repeated probe tones in high precision context elicited a suppression and rebound of the N2m source power. The differentiation suggested that the minimization of prediction error in low and high precision contexts likely involves distinct mechanisms.