Port State Control (PSC) is the inspection mechanism that ensures commercial vessels comply with internationally binding rules and regulations. During the PSC inspections, non-compliances with international maritime conventions may result in deficiencies or even the detention of the vessel. On the other side, deficiencies identified during PSC inspections are significant for the safe, secure, clean seas and sustainable marine environment. In this line, International Maritime Organization (IMO) aims to reduce ship-related pollution within the scope of the International Convention for the Prevention of Pollution from Ships (MARPOL). Specifically, AnnexVI is the most recently ratified regulation of MARPOL covering air pollution. Although Annex-VI deficiencies pose significant risks to maritime stakeholders and the natural environment, this topic has been broadly neglected by researchers. For this reason, a detailed risk analysis for the MARPOL Annex-VI deficiencies was carried out to demonstrate a prioritization concerning the marine environment and maritime stakeholders in this study. An improved Failure Mode and Effects Analysis (FMEA) approach is employed in the computation of risk priority numbers (RPN) by taking O, S, and D inputs from two different expert groups and the Paris MoU database. According to the results, the riskiest MARPOL Annex-VI failure modes are identified as 14615-Fuel change-over procedure (RPN: 235.71), 14608-Incinerator operations and operating manual (RPN: 232.65), and 14601-Technical files and if applicable, monitoring manual (RPN: 219.86). Consequently, the presented risk analysis and findings are intended to be a reference for maritime stakeholders to prevent harmful scenarios involving ship-related air pollution.