This paper addresses some concerns faced by the shipping industry nowadays. Initially, the environmental issues were resolved and stricter regulations are now being implemented with regards to the exhaust gas, specifically nitrogen oxides (NOx) and sulfur oxides (SOx), emitted from ships. Secondly, with the increasing and unstable cost of fuel oils in the world market, it has become almost a necessity to explore on a new alternative fuel. Hence, this study was conducted. An experiment was carried-out on a fishing survey vessel with the main engine (M/E) and generator engine (G/E) operated on expensive marine gas oil (MGO). During the experiment, two pre-refinery systems were installed and different fuel oil samples were employed for the M/E and the G/E. Furthermore, the NOx emission and soot concentration were monitored and verified. The results confirmed the compatibility of some fuel oil types to the engines and meeting the emission standards. MDO, MF15 and Bunker A can be used in place of MGO for the engines(M/E, G/E).