Interruption of prepared responses just before initiation is an important property of executive motor functions, and is known as motor inhibition. To clarify the mechanism of motor inhibition, we investigated the generators of reaction for suspending rapid repetitive movement using magnetoencephalography. Eleven subjects participated in this study and responded to tones. Oddball sequences composed of tones of 1 and 2 kHz were presented at a stimulus onset asynchrony (SOA) of 850 ms. A frequency of 80% was assigned randomly to each individual for either 1 or 2 kHz. Subjects were asked to make brisk right thumb flexion in response to frequent tones and not to move for rare tones. Source analysis with multiple equivalent current dipoles (ECDs) was conducted, and the resulting source locations and time courses were evaluated. The mean reaction time to frequent tones ranged from 168 to 267 ms, and the rate of successful stop after rare tones ranged from 84 to 96%. Generator source analysis revealed activation of bilateral auditory cortexes followed by activation around the left central area. Regarding central area activation, the primary motor and premotor areas were activated preferentially for frequent and rare tones, respectively. For rare tones, cortexes of other areas, such as the presupplementary and inferior frontal areas, were also activated in some subjects. The mean peak latency of the premotor area activity to stop movement for rare tones was 196 ms, whereas that of the primary motor area for motor response to frequent tones was 257 ms. The premotor area contralateral to the moving side plays an important role in inhibiting responses just before movement initiation.