Background: Fumigation of freight containers to prevent spread of pests and off-gassing of freight are sources of volatile chemicals that may constitute significant health risks when released. The aim of the study was to investigate the regulation and practice of container handling in Denmark with focus on preventive measures to reduce risk of chemical exposure. Methods: A comprehensive systematic search of scientific literature, legislation and recommendations related to safe work with transport containers from international and Danish regulatory bodies was performed. The practice of handling containers was investigated in a qualitative study based on a series of semi-structured interviews with key informants, including managers and health and safety representatives of organizations that handle containers. Results: Although several international and national regulations and local safety instructions relate to container handling, the provided information is not sufficiently detailed to conduct safe practice in many aspects. In accordance with the scientific literature, the interviewees estimate that there is a high frequency (5 to 50%) of containers with hazardous chemical exposure that are regarded as potentially damaging to health, although recognisable health effects are rare. There is limited knowledge about the types of chemicals, which mostly cannot be measured by available devices at the worksite. Aeration and use of personal protective equipment are typical preventive measures in practice, but their use is not consistent and does not necessarily ensure adequate protection. Conclusions: Managers, workers, even occupational health professionals have limited knowledge about the hazardous chemicals that can be released from containers. Detailed risk assessment and specific instructions on risk management are needed for safe handling of transport containers.