The Mærsk Mc-Kinney Møller Center for Zero Carbon Shipping (MMMCZCS) has published a paper Managing emissions from ammonia-fueled vessels explaining the need for multiple different treatment technologies to manage emissions. 

Ammonia slip from fuel handling operations or engine exhaust gas is highly toxic and represents a safety risk for crew and passengers. Other exhaust emissions include NOx formed by incomplete ammonia combustion and N2O, a potent greenhouse gas (1 gram of N2O is equivalent to 265 grams of CO2). Additionally, CO2 emissions will occur if a fossil-based pilot fuel is used.

Different emission management technologies will be needed onboard to treat ammonia boil-off gas (BOG) from fuel tanks, ammonia mixtures from purging and venting operations, and combustion emissions from engines. Some of these technologies are already commercially available for maritime use, including reliquefication and selective catalytic reduction (SCR). Others will need to be adapted for ammonia as a fuel, including gas combustion units/boilers, catalysts, and water catchers.