A technique which, when transporting a substrate from one module to another, detects a displacement of the substrate on a holding member and transfers the substrate to another module with the displacement within an acceptable range. Displacement of a wafer on a fork of a transport arm from a reference position is determined when the fork has received the wafer from one module and, when the displacement is within an acceptable range, the wafer is transported by the transport arm to another module. When the displacement is out of the acceptable range, the wafer is transported by the transport arm to a wafer stage module, and then the transport arm receives the wafer from the wafer stage module so that the displacement comes to fall within the acceptable range. The wafer can therefore be transferred to another module with the displacement within the acceptable range.