In this research, three dimensional mathematical models were developed to predict the shelf life of tofu packaged in a semi-rigid plastic container. A model combining oxygen transfer through the package and oxygen consumption within the package was considered. According to the results, the model simulations estimated that the number of microorganisms in the filled water was higher than that in the tofu, suggesting the shelf life of packaged tofu was not affected by the number of microorganisms in the tofu product, but rather by the number of organisms in the filled water. Additionally, the effects of the physical properties of the packaging material, such as oxygen permeability through the package, oxygen diffusion coefficient, the initial oxygen concentration in the filled water, and the depth of the filled water in the packaged tofu, were also observed.