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<div> Atmospheric pollutants from container terminal operations have adverse effects on the environment in port regions, leading to increased health risks, including respiratory and cardiovascular diseases among local residents. This paper aims to assess bio-efficiency for container terminals (CTs) in the presence of air emissions utilizing a slacks-based measure (SBM) model. In doing so, the paper first adopts cluster analysis to elect homogeneous CTs that aligns with the assumption of DEA theory, then uses a new method to estimate air emissions generated by CTs’ operations at harbor zones. Next, the SBM model is used to estimate the bio-efficiency of CTs in the presence of air emissions. Finally, CTs in the Ba Ria-Vung Tau port authorities (PAs) are employed as an empirical study to verify the proposed research model. The proposed research framework can contribute a methodological reference towards the relevant literature on abating atmospheric pollutants in maritime regions. </div>