National investment was performed in the research and development of renewable energy because of climate change by air pollution, exhaustion of energy sources, energy security, and so on. Biodiesel fuel of the renewable energy is highlighted as friendly environment energy, it is possible to operate in regular diesel engines when it is blended with invariable ratios without making any changes. Emission factors have been estimated for commercial ship from various research institutes; however, it is difficult to develop emission factors for military vessels. In this work, biodiesel blended fuel emission factors for sulfur dioxide and carbon dioxide were quantitatively estimated from propulsive diesel engine installed on naval vessel using fuel property analysis. In addition, exhaust emissions were quantitatively calculated on the basis of fuel consumption rate with biodiesel content by percentage.