The new type closed-path CO2/H2O infrared gas analyser enables us to calculate CO2 fluxes from both the mixing ratio () and mass density of CO2 (). After the WPL correction was applied, and were almost in accord with each other. However, tended to be slightly larger than , which resulted in a significant difference in cumulative CO2 fluxes. We found that this difference was explained by the pressure covariance term, which is normally omitted in the WPL correction. Therefore, ignoring the pressure covariance term in the WPL correction can cause a serious error in estimation of annual net ecosystem exchange. To reduce uncertainties in calculations, we recommend using the mixing ratio for calculation of CO2 fluxes when using the new type closed-path infrared gas analyser.