If a plurality of wafers are placed on each shelf of a rack in a pod, some problems will arise in processing processes. In addition, in some apparatus for detecting wafers, driving means having a not so high stability in the speed such as an air-operated cylinder is used for moving the sensor, in order to make the structure simple. In the case that detection is performed while the sensor is moved by such driving means, errors becomes large and it is difficult to detect wafers accurately. The present invention provides a wafer processing apparatus provided with a transmissive wafer detection sensor, a dog having index means and a transmissive sensor for the dog. The wafer processing apparatus calculates the ratio of the duration time of a signal from the transmissive wafer detection sensor and the duration time of a signal from the transmissive sensor for the dog corresponding to the index means and compares the ratio with a threshold value set in advance to determine the number of wafers.