Rapid depletion of petroleum reserves, stringent emission legislations and global warming has given us an opportunity to find biodiesel as an alternative to diesel fuel. Biodiesel is a biogradable, renewable, sulphur free, non-toxic, and oxygenated green fuel. Recent emission legislations have also restricted the nano particles emission in addition to particulate matter, due to their adverse impact on health. Karanja and Jatropha oils are non-edible vegetable oils. Karanja and Jatropha oil methyl ester biodiesel are prepared by the process of transesterification. Biodiesel emits lesser gaseous emission as compared to diesel fuel. However, the only major concern in the use of biodiesel is that it increases NOx emission. Nano particle fuel additive is one of the essential techniques to overcome the NOx emission drawback of biodiesel. In the present study, the engine performance and emission of CO, UHC, NOx and PM including nano particle emission, were compared for diesel, Karanja and Jatropha oil biodiesel with Cerium Oxide nano particles fuel additive, in a 12-cylinder, 585 kW, CIDI military heavy-duty diesel engine. The experimental results showed that engine performance with Karanja and Jatropha oil biodiesel with fuel additive, increased by 3-4%, along with lower gaseous emission including 15% - 25% lower NOx emission and lower nano particles emission, as compared to mineral diesel fuel.