Gaseous fuels have many advantages than liquid fuels, as their calorific values of fuels are high, pollutants emitted by gaseous fuels are low and less dangerous when compared with liquid fuels. The drawbacks associated with use of vegetable oils in diesel engines such as high viscosity and low volatility can be reduced to some extent by converting them into biodiesel. However, they (biodiesel) cause combustion problems in diesel engine, due to their moderate viscosity, and hence call for low heat rejection (LHR) engine, which can burn low calorific value fuel, give high heat release rate and faster rate of combustion. The concept of LHR engine is to minimize heat loss to the coolant, thereby increasing thermal efficiency. LHR engine in this investigation consisted of ceramic coated diesel engine. They are many methods toinduct gaseous fuels such as port injection, carburetion technique, injection of gaseous fuel at the near endof compression stroke etc,. Investigations were carried out with biogas gas as primary fuel inducted by port injection and cottonseed biodiesel was injected into the engine in conventional manner, as India is second large producer of cottonseed oil in the world. Particulate matter (PM), oxides of nitrogen (NOx), carbon mono oxide (CO) levels and un-burnt hydro carbons (UBHC) are the exhaust emissions from a diesel engine. They cause health hazards, once they are inhaled in. They also cause environmental effects like Green-house effect and Global Warming. Hence control of these emissions is an immediate effect and an urgent step. The pollutants of PM, NOx ,CO and UBHC were determined at full load operation of the engine with varied injection timing such as recommended injection timing and optimum injection timing. NOx levels were reduced with provision of exhaust gas recirculation (EGR) at optimum flow rate of 10%. The maximum induction of biogas with conventional engine (CE) was 35% of total mass of biodiesel as full load operation, while it was 45% with LHR engine. Particulate emissions were determined by AVL Smoke meter, while other emissions were measured by Netel Chromatograph multi-gas analyzer at full load operation. These pollutants were drastically reduced with induction of biogas and further reduced with advanced injection timing. NOx levels drastically reduced with EGR.