Most information on estimating greenhouse gas fluxes from soils is obtained by using chamber techniques. Closed chamber is more widely applied because of its simple design, low cost, and high sensitivity. In this study, major rice growth characteristics and yield were compared between inside and outside a closed chamber after a seasonal gas flux measurement. Results showed that the rice yield in the chamber-covered site was significantly (P < 0.01) reduced by about 30% comparing to the undisturbed site outside the chamber. There was no significant difference in the rice plant height, total rice straw weight, spike length, and average grain weight between the chamber-covered and undisturbed sites. Elevated temperature during the gas flux measurement was probably the major reason for the observed yield decrease, which might sterilize the rice reproductive organs. We found that CO₂ and CH₄ emission rates remained the same before and after cutting the above water part of the rice plants. The ratio of CO₂ and CH₄ emission rates was used to estimate the percentage of CH₄ in total CO₂ and CH₄ emissions from the rice fields. Regression analysis indicated that CH₄-C emissions accounted for 13.4% of the total CO₂ and CH₄-C emissions during the major rice-growing season. The implication of rice yield decrease by chamber enclosure is that more plant photosynthesis products may be released into the rice soils to support greater CH₄ production. The results of this study indicate a possible adverse effect of chamber technique on CH₄ measurement by overestimating its flux rate in flooded rice fields.