A dedicated system for airborne ship emission measurements of SO2, NOx and particles has been developed and used from several small aircraft. The system has been adapted for fast response measurements at 1 Hz, and the use of several of the instruments is unique. The uncertainty of the given data is about 20% for SO2 and 24% for NOx emission factors. The mean values with one standard deviation for multiple measurements of 158 ships measured from the air on the Baltic and North Sea during 2011 and 2012 show emission factors of 18.8 ± 6.5 g kg−1 fuel , 66.6 ± 23.4 g kg−1 fuel and 1.8 ± 1.3 1016 particles kg−1 fuel for SO2, NOx and particle number, respectively. The particle size distributions were measured for particle diameters between 15 and 560 nm. The mean sizes of the particles are between 45 and 54 nm dependent on the distance to the source, and the number size distribution is monomodal. Concerning the sulfur fuel content, around 85% of the monitored ships comply with the International Maritime Organization (IMO) limits. The reduction of the sulfur emission control area (SECA) limit from 1.5 to 1% in 2010 appears to have contributed to reduction of sulfur emissions that were measured in earlier studies from 2007 to 2009. The presented method can be implemented for regular ship compliance monitoring.