According to one embodiment, a model generation system includes a NCLM processor, a filter part, a model generator, a variable narrow-down part, a determiner, and a soundness calculator. The NCLM processor and the filter part narrows down a first input variable group to a third input variable group selected using NCLM. The model generator generates a model of a relationship between the third input variable group and an output variable. The variable narrow-down part narrows down the first input variable group to one or more of the input variables not used in the generation of the model. When the number of the models has not reached the specified number, the determiner outputting to the NCLM processor the first input variable group narrowed down by the variable narrow-down part. The soundness calculator calculates an overall soundness of the models and calculating a soundness of each of the models.