Rapid depletion of fossil fuels is urgently demanding an extensive research work to find out the viable alternative fuel for meeting sustainable energy demand without any environmental impact. In the future, our energy systems will need to be renewable, sustainable, efficient, cost-effective, convenient and safe. Therefore, researchers has shown interest towards alternative fuels like vegetable oils, alcohols, LPG, CNG, Producer gas, biogas in order to substitute conventional fuel i.e. diesel used in compression ignition (CI) engine. However, studies have suggested that trans-esterified vegetable oils retain quite similar physico-chemical properties comparable to diesel. Besides having several advantages, its use is restricted due to higher emissions i.e. NOx, CO, HC and deposits due to improper combustion. Hence, there is a need of cleaner fuel for diesel engines for the forthcoming stringent emissions norms and the fossil depletion. In the current exhaustive investigation CNG is used with Karanja oil methyl ester (KOME) in a dual fuel mode for complete combustion of charge present inside the combustion chamber, and for the reduction of emissions associated with CI engines. For that CNG is fed to engine along with air through inlet manifold during the suction stroke. In order to initiate the combustion of CNG charge a small pilot injection of KOME is injected during the end of compression stroke, which have high volatility with low auto ignition temperature. The engine trials were conducted on a stationary air cooled constant speed agricultural direct injection diesel engine by increasing load from 25-100%.The effects of the pilot charge on various performance and emission characteristics were evaluated on all range of load. While comparing the results with diesel an increment in Brake Thermal Efficiency (BTE) and reduction in the emissions i.e. CO, HC, smoke were found with the dual fuel mode of CNG-KOME in CI engine.