To determine the means and variations in CH4 uptake and N2O emission in the dominant soil and vegetation types to enable estimation of annual gases fluxes in the forest land of Japan, we measured monthly fluxes of both gases using a closed-chamber technique at 26 sites throughout Japan over 2 years. No clear seasonal changes in CH4 uptake rates were observed at most sites. N2O emission was mostly low throughout the year, but was higher in summer at most sites. The annual mean rates of CH4 uptake and N2O emission (all sites combined) were 66 (2.9–175) µg CH4-C m−2 h−1 and 1.88 (0.17–12.5) µg N2O-N m−2 h−1, respectively. Annual changes in these fluxes over the 2 years were small. Significant differences in CH4 uptake were found among soil types (P < 0.05). The mean CH4 uptake rates (µg CH4-C m−2 h−1) were as follows: Black soil (95 ± 39, mean ± standard deviation [SD]) > Brown forest soil (60 ± 27) ≥ other soils (20 ± 24). N2O emission rates differed significantly among vegetation types (P < 0.05). The mean N2O emission rates (µg N2O-N m−2 h−1) were as follows: Japanese cedar (4.0 ± 2.3) ≥ Japanese cypress (2.6 ± 3.4) > hardwoods (0.8 ± 2.2) = other conifers (0.7 ± 1.4). The CH4 uptake rates in Japanese temperate forests were relatively higher than those in Europe and the USA (11–43 µg CH4-C m−2 h−1), and the N2O emission rates in Japan were lower than those reported for temperate forests (0.23–252 µg N2O-N m−2 h−1). Using land area data of vegetation cover and soil distribution, the amount of annual CH4 uptake and N2O emission in the Japanese forest land was estimated to be 124 Gg CH4-C year−1 with 39% uncertainty and 3.3 Gg N2O-N year−1 with 76% uncertainty, respectively.