Abstract Carbon accounting is a key issue in the discussions on global warming/CO 2 mitigation. This paper applies both the intergovernmental panel on climate change-reference approach (IPCC-RA) and the non-energy use emission accounting tables (NEAT) model, a material flow analysis, to estimate the carbon storage originating from the non-energy use as to assess the carbon release from the use of fossil fuels in Korea for the years 1999 and 2000. The current Korean carbon accounting seems to overestimate the carbon storage and to concomitantly underestimate CO 2 emissions. This is because the gross naphtha deliveries are currently considered as feedstock use. The estimation after correction of the non-energy use statistics shows, however, that the carbon storage calculated according to the IPCC-RA are lower than those calculated using the NEAT model. This is because the IPCC default storage fraction for naphtha used in Korea seems to be too low for the Korean petrochemical production structure. A by-product of this study is the identification of a double counting of naphtha consumption in the amount of the backflows to refineries in the Korean energy balance which led to a four-year project to revise the energy balances back to 1990. This paper shows that a material flow analysis like the NEAT model can provide a better basis for estimation of CO 2 emissions of the non-energy use and with it that of the fossil fuel use than the current IPCC-RA. The NEAT model can be used as an independent emission calculation tool to verify the IPCC-RA and IPCC-SA as well as to replace them.