There is provided a flexible manufacturing system that can reliably place a workpiece that isn't defective piece in a state where the workpiece will be machined again. After a pallet is conveyed to a standby position and before machining of the workpiece attached to the pallet is started, controllers determines whether machining of the workpiece with a corresponding machining device is possible. When it is determined that machining is possible, the controller starts machining with the machining device. When it is determined that machining is impossible, the controller make a conveyor convey the pallet from the standby position to a pallet storage room, and stores the machining status information on the conveyed pallet as the machining-waiting state.