This paper considers the part input problem of a production system where two Flexible Transfer Lines (FTLs) consisting of an up-stream production line and a down-stream production line while operating under Just In Time (JIT) production management. The up-stream production line processes the raw material after receiving them from suppliers, and after processing them, delivers the processed product to a down-stream production line via a conveyer. In this paper, we have proposed a novel idea for a part input real time control system, known as Algorithm for Real Time Control of Part Input Systems (ARTCOPS). The algorithm is useful when FTLs are in operation under a production order that is different from the pre-decided production schedule. Simulations of virtual production systems have been carried out to verify that ARTCOPS is useful in real time control, although the production orders are different from the pre-decided production scheduling.