Uncertainty about efficiency and sustainability of shrimp production due to diseases and climatic events may prevent Vietnam from attaining US $10 million target from shrimp exports by 2025. We surveyed 120 and 159 shrimp farmers from Khánh Hòa and Trà Vinh provinces, respectively, to obtain information on their input use, production levels and the effects of diseases and climate change events on their farm profitability. Stochastic production frontier analysis (SFA) discovered that the number of workers, crops and seed costs positively influenced farmers’ profits, while cost of chemicals and labour negatively affected the profit of Khánh Hòa farmers. The number of workers and chemical costs positively affected profits in Trà Vinh, while cost of labour and energy, the number of crops and average stocking density negatively influenced farmer profit in Trà Vinh. Number of years of schooling, experience and average size of ponds positively influenced economic efficiency, while the number of ponds and climatic change events negatively influenced efficiency in Khánh Hòa province. Age and alternative power source positively affected economic efficiency, while disease prevalence affected efficiency of Trà Vinh. All farms practicing intensive or extensive shrimp production achieved 90% efficiency. The government should encourage the wise use of resources, high-quality seeds and a sensitive balance between intensive and extensive culture to sustainably attain its national production and export goals.