This study aims to examine total factor productivity (TFP) and its determinants in offshore fisheries under the worsening fishing environment and to propose policy improvement based on the estimation results. We identified a decline in TFP of offshore fisheries from 2012 to 2020 employing the global Malmquist productivity index (GMPI), with the primary cause being the regression of the production possibility frontier due to the reduction of fishery resources. Moreover, utilizing the system generalized method of moments (GMM), we found that the determinants, such as the cessation of operations in Japan’s EEZ, vessel age, fishing experience, and oil prices, contribute to a decrease in the TFP of offshore fisheries. Therefore, this study suggests implementing a total allowable catch (TAC)-centered fishery resource management policy, along with reducing loan interest rates and extending the repayment period for the vessel modernization project. Furthermore, it is necessary to improve the TFP of offshore fisheries by providing regular training for fishermen, implementing the tax-free petroleum stockpiling project, and developing alternative fishing grounds.