While maritime shipping is currently the most reliable form of cargo transport for global trade, it causes significant air pollution. The number of inbound and outbound vessels in the Port of Kaohsiung, as well as the cargo throughput, is the highest in Taiwan. These vessels emit considerable amounts of air pollutants. Two methods based on vessel activity intensity were adopted in this study to estimate the emissions of sulfur dioxide (SO2) generated by the consumption of fuel oils by merchant vessels in the Port of Kaohsiung from 2006 to 2010. Emissions were estimated to be 3,229–3,889 tonnes and 1,395–1,777 tonnes using a method based on cargo capacity and vessel engine activity time, respectively. These estimates are equivalent to 3.7% to 4.5% of the overall SO2 emissions in Kaohsiung City. The difference between these estimates was due to varying parameters being adopted for each method, such as cargo throughput capacity, vessel power and the emission correction factor related to fuel oils. The SO2 emissions of merchant vessels can be mitigated with the use of an incentive discount system. It is also estimated that when the shore power facilities in the Port of Kaohsiung are used to reduce emissions during vessel hotelling, the additional power requirement would be 6.6% of the overall power consumption of Kaohsiung City for the year 2010.