Emissions from ships at berth are small compared to the total ship emissions; however, they are one of the main contributors to pollutants in the air of densely-populated areas, consequently heavily affecting public health. This is due to auxiliary marine engines being used to generate electric power and steam for heating and providing services. The present study has been conducted on an engine representative of a marine auxiliary, which was a heavy duty, six-cylinder, turbocharged and after-cooled engine with a high pressure common rail injection system. Engine performance and emission characterisations during cold start are the focus of this paper, since cold start is significantly influential. Three tested fuels were used, including the reference diesel and two IMO (International Maritime Organization) compliant spiked fuels. The research engine was operated at a constant speed and 25% load condition after 12 h cooled soak. Results show that during cold start, significant heat generated from combustion is used to heat the engine block, coolant and lubricant. During the first minute, compared to the second minute, emissions of particle number (PN), carbon monoxide (CO), particulate matter (PM), and nitrogen oxides (NOx) were approximately 10, 4, 2 and 1.5 times higher, respectively. The engine control unit (ECU) plays a vital role in reducing engine emissions by changing the engine injection strategy based on the engine coolant temperature. IMO-compliant fuels, which were higher viscosity fuels associated with high sulphur content, resulted in an engine emission increase during cold start. It should be taken into account that auxiliary marine diesel engines, working at partial load conditions during cold start, contribute considerably to emissions in coastal areas. It demonstrates a need to implement practical measures, such as engine pre-heating, to obtain both environmental and public health advantages in coastal areas.