According to one embodiment, a manufacturing apparatus control system includes a defect rate detector, a significant difference tester and a defect determining unit. The defect rate detector extracts a first apparatus passage history having a first defect rate. The defect rate detector detects a third defect rate by excluding a second apparatus passage history having a second defect rate from the first apparatus passage history. The significant difference tester calculates a significant difference test value. The defect determining unit extracts a third apparatus passage history based on the third defect rate and the significant difference test value.