Total emissions from enteric fermentation was identified as a key category in Japan’s 1990 inventory, and are still a key category in the latest inventory submission (NIR 2018). Nitrous oxide from manure management, but not methane from manure management, is a key category. Japan reports enteric fermentation emissions from dairy and non-dairy cattle using a Tier 2 approach. A Tier 1 approach is used for enteric fermentation from all other livestock types. Methane emissions from manure management are estimated using a Tier 2 approach with a combination of country-specific and default emission factors, depending on the manure management system. Japan’s specific approach adopted for both enteric fermentation and manure management methane emissions has evolved over time. This case study describes the countries approach for cattle, poultry and swine.