Although the Japanese feed-in tariff was introduced to expand renewable energy, leading to the expansion of palm kernel shell (PKS) use, the greenhouse gas (GHG) emission reduction effect is evaluated using the limited life-cycle of PKS, focusing on processes after PKS generation point. Therefore, this study aimed to elucidate the life-cycle GHG emissions of power generation using PKS. We targeted two PKS-firing power plants as these are the first two instances of the use of PKS in power plants in Japan. A system boundary was established to cover palm plantation management in Indonesia and Malaysia, as both power plants import PKS from these countries. The GHG emissions were derived from land-use change, palm plantation, oil extraction, PKS transportation, and power plants. Six scenarios were examined for the emissions based on the type of land-use change and the existence of biogas capture in oil extraction. CO2 emissions from PKS combustion were also calculated by assuming that carbon neutrality was lost because of cultivation abandonment. The GHG emissions in one scenario, where the plantations were replanted and continuously managed and no biogas capture implemented in oil extraction, exhibited an average of 0.134 kg-CO2eq/kWh reduction in a plant in Kyushu District, and 0.043 kg-CO2eq/kWh reduction in a plant in Shikoku District for liquid natural gas-fired steam power generation, respectively. More than 65% of life-cycle GHG emissions originate from biogas generated during oil extraction; thus, biogas capture is an effective strategy to reduce current emissions. In contrast, in the case of accompanying land-use change or collapse of carbon neutrality, the emissions considerably exceeded those of fossil fuels. These findings indicated that the FIT fails to consider the risk of increased emissions or further substantial emission reductions. Therefore, the feasibility of FIT application to PKS needs to be re-established by evaluating the entire PKS life-cycle.