Seeking alternative sources of energy for its more effective use, reducing emissions of toxic pollutants to the atmosphere and counteracting global warming are nowadays the major areas of development in the power industry, including the design of combustion engines. Currently, the research into the use of new fuels, which may be effective sources of energy, is performed by many scientific centres. The use of biogas for production of energy in cogeneration systems is one of the ways for improvement of energy balance. In the research described herein, a dual-fuel compression ignition engine was fuelled with gaseous fuel with variable CNG and CO2 ratios. The tests were performed for engine fuelling controlled by both an original controller with the software optimised for single-fuel operation and for the injection of a pilot dose of diesel controlled by a dedicated controller enabling the adjustment and control of the injection and dose parameters. This paper presents the effect of carbon dioxide content in gaseous fuel on the combustion process and emission of toxic compounds in the engine examined.