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Addressing the urgent global challenge of man-made greenhouse gas emissions and climate change necessitates collaborative action between shipping lines and government regulatory agencies. Aligning with the International Maritime Organization’s emissions reduction strategy, this paper presents a novel bi-level programming model that unifies these stakeholders. On the upper level of the proposed bi-level model, a number of shipping lines optimize retrofitting plans for their vessels to maximize economic benefits. On the lower level, the regulatory agency responds to the carbon reduction efforts by setting retrofitting subsidies and emission penalty rates. This framework represents a multi-leader–single-follower game involving shipping lines and the regulatory agency, and its equilibrium is determined through an equilibrium problem with equilibrium constraints (EPEC). The EPEC comprises multiple single-leader–follower problems, each of which can be formulated as a mathematical program with equilibrium constraints (MPEC). The diagonalization algorithm (DM) is employed for its solution. Simulation studies performed based on a ten-year planning period show that the proposed approach can effectively promote vessel retrofitting and the use of green fuels, which leads to an annual emission reduction of over 50%.