To elucidate the mechanisms underlying sensorimotor integration, we investigated modulation in the primary (SI) and secondary (SII) somatosensory cortices during the preparatory period of a self-initiated finger extension. Electrical stimulation of the right median nerve was applied continuously, while the subjects performed a self-initiated finger extension and were instructed not to pay attention to the stimulation. The preparatory period was divided into five sub-periods from the onset of the electromyogram to 3000 ms before movement and the magnetoencephalogram signals following stimulation in each sub-period were averaged. Multiple source analysis indicated that the equivalent current dipoles (ECDs) were located in SI and bilateral SII. Although the ECD moment for N20m (the upward deflection peaking at around 20 ms) was not significantly changed, that for P30m (the downward deflection peaking at around 30 m) was significantly smaller in the 0- to −500-ms sub-period than the −2000- to −3000-ms sub-period. As for SII, the ECD moment for the SII ipsilateral to movement showed no significant change, while that for the contralateral SII was significantly larger in the 0- to −500-ms sub-period than the −1500- to −2000-ms or −2000- to −3000-ms sub-period. The opposite effects of movement on SI and SII cortices indicated that these cortical areas play a different role in the function of the sensorimotor integration and are affected differently by the centrifugal process.