The NEAT model (Nonenergy-use Emission Accounting Tables) has been developed in order to estimate CO2 emissions caused by so-called nonenergy use of fossil fuels. The model is based on material flow accounting. The model has been applied to a number of countries in order to validate and improve its use. This paper discusses the case study for Japan. The NEAT analysis suggests that emissions in 1996 were 23 Mt higher than previously estimated based on the guidelines of the Intergovernmental Panel on Climate Change (IPCC). This quantity equals 1.9% of the total Japanese greenhouse gas emission. It is recommended to adjust the Japanese emission accounting practice and to apply more detailed emission estimation methods in future years. Given similar results for other countries it is also recommended to improve the IPCC guidelines.