Long term fisheries observer data were used to analyse the influence of a range of environmental variables and mitigation measures upon catch rates of seabirds in the Japanese pelagic longline fishery. In the Australian Fishing Zone (AFZ) seabirds were most likely to be caught on longlines that were set during summer, in southern areas of the zone, and during daylight hours. However, interpretation of changes in catch rates resulting from the use of mitigation measures or from weather effects were problematic due to the interrelationships between the many measured factors. Interpretation and accurate assessment was further complicated by ongoing changes to fishing practices and equipment, and due to changes of the priority that fisheries observers placed on the collection of seabird data. The data relating to factors affecting seabird bycatch which is currently collected incidentally by fisheries observers are not sufficiently robust to allow confidence in statistical assessments alone to examine the efficacy of mitigation measures. Dedicated observations may allow for more confident determination of the reasons why seabirds were or were not caught, and to what degree mitigation measures are effective. The use of these observations in combination with the analyses suggested seabird bycatch rates may be lowered by the use of bird lines, bait throwing machines and thawed baits. However, appropriate use and deployment of these measures are critical if they are to be effective. Further work is required to better understand the effect of these measures, and their effect upon the catch rate of target and non-target species.