Several factors can affect occupational accident frequency, namely economical factors, technologies used (low automation, discontinuous operating) job design, organization of work/environmental conditions and human factors. In particular, technological advances in industrial activities can give rise to improvement in productivity and in occupational health and safety, but not necessarily simultaneously. The beginning of the container transport dates back to 50 years ago, but while containerization changed everything, from ships and ports to patterns of global trade, its impact on work injuries was not explored at all. The aim of this paper is to investigate the relationship between work organization, job experience, productivity and occupational accidents, from the starting of the container expansion to nowadays, considering Genoa port (Italy), one of the largest of the Mediterranean Sea. In order to minimize possible reporting biases, such as underreporting or reclassification to a lower level of severity, injury statistics are elaborated starting from data collected directly on-site, from internal accident or medical-aid reports. An in-depth statistical analysis on occupational injuries in the years 1980–2006 is carried out, with reference to frequency indexes, mechanism of injury and material causes. The increase of container-ships traffic and, consequently, the sharp change in port infrastructure involved a rapid modification also in the work organization, with particular reference to the number and characteristics of workforce (decrease from 5783 to nearly 1000 employees and increase of low experience workers from 28% to 74%). The striking high percentage increase of young or low experienced workers in handling container (and performing correlated new tasks) caused a remarkable increase of the risk for occupational injuries. In the studied port, we recorded an increase of the frequency index (injuries per hundred thousand hours worked) from 13.0 to 29.7. It results that the increased expansion of shipping container utilization is not connected to a correspondent human factor safety implementation. Main risk factors are pointed out, revealing an increase of accidents due to transport vehicle (+8.3%) and a reduction of accidents caused by substance or materials (−4.5%). These factors show a statistical significant correlation with the new job tasks. Consideration of these findings may enable managerial solutions and workplace organization interventions for the prevention of injuries and safety performance improvement in port activities.