Introduction Fishery is a hazardous industry with high occupational fatalities, mainly due to vessel disasters, especially among smaller vessels, according to European and North-American studies. However, Asian countries with different industry status and larger portion of global marine capture production are short of adequate investigation.

Methods In Taiwan, Fisheries Agency provided compensation for maritime fatalities and capsizing vessels, and recorded all enrolled crews and fishing vessels in Fishery Administration Management Information System. Using these two databases, incidence rate and odds ratio (OR) were calculated to depict an overall picture of maritime fatal accidents and associated causal factors.

Results From 2003 to 2015, there were 562 cases of fatal accidents, whose mechanisms were man overboard (368, 65.5%), followed by capsizing (53, 9.4%). Overall incidence rate was 3.6 per 10 000 man-labour year. The rates were 2.51, 4.12, and 7.28 per 10 000 man-labour year, and odds ratios were 1.0, 1.64 and 2.90, for coastal (<12 Nautical miles, Nm), inshore (12–200 Nm), and deep sea (>200 Nm) fisheries.

There were 632 cases of vessel capsizing, whose mechanisms were fire (162, 25.63%), followed by natural disaster, mechanical problem (85, 13.45%), and collision (71, 11.23%). Overall incidence rate was 152.01 per 10 000 vessels. The rates were 7.15, 21.42, 71.48, and 51.95 per 10 000 vessels, and odds ratios were 1.0, 3.00, 10.05 and 7.29, for small-sized (sampan and fishing raft), small-medium-sized (<20 gross registered tonnages, GRT), medium-large-sized (20–200 GRT) and large-sized (>200 GRT) vessels.

Conclusion Our findings showed the mixed effect of vessel size and fishery types on maritime fatal accidents, and deep-sea medium-large-sized vessels, as the smallest vessels in deep sea fisheries, had the highest risk. Compared with other developed countries, more than half fishing vessels of deep sea fisheries in Taiwan are less than 100 GRT, and preventive intervention should be focused on these vessels.