A facility control system comprises a selection processing portion that selects, based on a manual operation and when an abnormal condition occurs in a second-layer computer that issues a task command to a first-layer program which issues an apparatus operating command to an apparatus controller, whether to cause a first-layer computer to execute a second-layer program that had been executed by the second-layer computer, and a substitute command output processing portion which outputs a substitute command in accordance with selection information selected by the selection processing portion. The first-layer computer executes the second-layer program that had been executed by the second-layer computer in which the abnormal condition occurred based on a substitute command outputted by the substitute command output processing portion.