Global warming due to engine exhaust pollution, rapid depletion of petroleum oil reserves, and stringent regulation on emission has compelled researchers to find bio fuels as alternative to diesel fuel. Biodiesel is an oxygenated, sulphur free, non-toxic, biogradable, and renewable fuel. Biodiesel can be produced from non-edible vegetable oil using Elgae, Jatropha and Karanja oil. Biodiesel is a green fuel except it emit 15-25% more NOx in compared to diesel fuel. Nano particle emission is more harmful to human being. Nano particle emission of biodiesel to be measured now as per new stringent regulation. Elgae, Jatropha and Karanja oil methyl ester biodiesel have comparable engine performance and low exhaust emission characteristics, except for NOx emission, in comparison to diesel fuel. In this study, engine performance, combustion and engine emissions of CO, CO2 UBHC, NOx and PM including nano particle emission characteristics, were compared for Elgae, Jatropha, and Karanja oil biodiesel fuels by using Cerium oxide nano particle fuel additive in a Military, heavy- duty, 582kW, compressed ignition diesel injection (CIDI) diesel engine. In the test investigation engine performance with Elgae, Jatropha and Karanja oil biodiesel fuels were found slightly lower in comparison to diesel fuel. All three tested biodiesel fuels blended with Cerium oxide nano particles fuel additive, have produced lower engine exhaust emissions including 22-26% lower NOx emission along with lower nano particulate emissions, as compared to diesel fuel.