A system, method, apparatus and program which enables the automation of the carrying of a lot or lots of special purpose wafers between stockers and to achieve high speed processing while suppressing an increase in storage volume. The carrying control system includes stockers for storing therein special purpose lot or lots comprising wafers which will not be processed in production facilities, or said special purpose lot or lots and usual lot or lots comprising wafers which will be processed by production facilities and a carrying host computer for controlling automatic carrying of lot or lots in carrying facilities. The carrying host computer receives a report of receipt of the special purpose lot(s) by one of stockers transmitted from the one of the stockers when the special purpose lot(s) is received by said one of the stocker in said carrying pattern, for initiating a timer and for assuming that processing of the special purpose lot(s) stored in said stocker is completed when a result of count in the timer shows lapse of a predetermined period of time, for determining a next stocker to which the special purpose lot is to be carried next in accordance with a carrying pattern corresponding to the special purpose lot(s) stored in the storage unit, and for sending to the one of the stockers which stores the special purpose lots an carrying instruction for carrying special purpose lots to next stocker.