Major rice growth characteristics and grain yield were compared between inside and outside of a chamber coverage area after a seasonal CH4 and N2O flux measurement using a closed chamber technique. Results show that only grain yield was significantly (P<0.01) reduced by chamber enclosure. There was no significant difference (P>0.05) in plant height, total straw weight, spike length, and average grain weight. Temperature increase during the gas flux measurement was likely the major cause for the observed grain yield decrease by sterilizing rice reproductive organs. Methane flux rates from rice fields were likely overestimated by using closed chamber technique because decreasing grain yield by chamber enclosure may result in more plant photosynthesis products released into soils to enhance CH4 production. Analyzing CH4 and CO2 emission ratio from the rice field, after cutting the above-water part of rice plants, indicated that CH4–C emission accounted for approximately 13% of the total CO2 and CH4–C emission during the major rice growing season.