The new type closed-path CO2/H2O infrared gas analyser enables us to calculate CO2 fluxes from both the mixing ratio (inline image) and mass density of CO2 (inline image). After the WPL correction was applied, inline image and inline image were almost in accord with each other. However, inline image tended to be slightly larger than inline image, 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.