A modified closed-chamber method for estimating total, plant-mediated, and bubbling (ebullition) emissions of CH4 from rice paddies has been developed to use high-time-resolution CH4 concentration data (-1 Hz) obtained by a spectroscopic mobile gas analyzer. Here we aimed at determining an appropriate minimum time length of chamber closure for accurate flux measurement by investigating 3255 datasets obtained from a 2-year field survey. To investigate the minimum time length for each chamber measurement, we generated a series of datasets from each measurement: by setting the hypothetical termination time of the chamber closure ahead in 1-min intervals, we obtained various chamber CH4 concentration time series with different durations of chamber closure, and separately estimated CH4 emissions via rice plants and bubbling from each. The estimated flux was sensitive to time length with short closure times, but became less sensitive with longer closure. We defined the minimum time length at which the difference in estimated flux between adjacent time windows was small enough ( 10% of plant-mediated emission). The estimated minimum time length differed from one measurement to another, but 10 min was sufficient for 99% of cases. Detailed analysis showed a positive correlation between minimum time length and frequency of bubbling events; the time length needed to be longer as bubbling events became more frequent. From this relationship, we computed the appropriate chamber-duration time as a function of bubbling frequency. In the absence of ebullition, 4-5 min was sufficient, but as the bubbling frequency increased to 2.5 times per minute 15-20 min was necessary for accurate pathway-dependent flux measurements.