Vehicular exhaust emission control and engine efficiency are the most important parameters in current engine design. The Euro V emission norms are directing the research towards developing new technologies for combating engine emissions. Natural gas has become a widely used alternative fuel due to its many advantages including its ready availability and its low emission levels. Addition of hydrogen to CNG improves the composition and properties of base fuel CNG. In the present work a diesel engine was converted to operate in dual fuel engine mode in which Hydrogen-compressed natural gas (HCNG) was injected into the intake manifold using a specially developed electronic control unit (ECU) while diesel/biodiesel was injected directly inside the combustion chamber during the compression stroke. Experimental investigations were then carried out on a single cylinder four stroke CI engine test rig operated in dual fuel mode using Diesel, Honge methyl ester (HOME), Jatropha methyl ester (JOME) as injected pilot fuels and HCNG as injected primary fuel. ECU was used for varying the injection timings and injection durations for HCNG 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 HCNG flow rate was maintained at 0.5kg/h. The experimental results showed that an injection timing of 5 o bTDC and injection duration of 40 o bTDC for HCNG injection was found to be optimum based on the improved performance, combustion and emission characteristics. The brake thermal efficiency for manifold injected HCNG dual fuel operation with diesel, HOME and JOME at 80% load was found to be 28.1%, 27.2% and 26.2% respectively. The Smoke emissions, Carbon monoxide (CO), Carbon dioxide (CO2) emissions were found to be lesser with an injection timing of 5 o bTDC and injection duration of 40 o bTDC in HCNG injected dual fuel operation. The use of HCNG manifold injection in the dual fuel operated CI engine improves the performance and reduces the exhaust emissions from the engine except for HC and NOX emissions.