Energy demand at a global level is increasing day by day and fossil fuel resources are on the verge of becoming extinct. The drastic increase of the oil prices in the global oil market and the increased pollution levels created an interest to find renewable, sustainable and alternative fuels. Natural gas (NG) is considered as a most prominent alternative fuel due to its many advantages including its ready availability and its low emission levels. A diesel engine was converted to operate in dual fuel engine mode in which compressed natural gas (CNG) was injected using a specially developed electronic control unit (ECU) into the intake manifold while injected pilot biodiesel auto ignites and it becomes a source of ignition for CNG. Experimental investigations were conducted over a single cylinder water cooled four stroke dual fuel CI engine test rig operated using diesel, honge methyl ester (HOME), jatropha methyl ester (JOME) and their blends with 15% ethanol as injected pilot fuels and CNG as injected primary fuel. ECU was used for varying the injection timings and injection durations for CNG injection while the optimum injection timing for diesel/biodiesel was maintained at 27°bTDC. The pilot fuel injection pressure was maintained at 230 bar. Engine was operated with constant compression ratio of 17.5 and CNG flow rate was maintained at 0.5 kg/h. The experimental results showed that an injection timing of 5 o bTDC and injection duration of 60 o CA for CNG injection was found to be optimum based on the improved performance, combustion and emission characteristics. The brake thermal efficiency for manifold injected CNG-diesel/biodiesel-ethanol blended dual fuel operation at 80% load was found to be 27.1%, 26.2% and 25.2% for diesel-ethanol blend, HOME-ethanol blend and JOME-ethanol blends respectively. The carbon exhaust emissions and smoke emissions were found to be lesser in CNG injected dual fuel operation compared to CNG inducted dual fuel operation.