A method of operating a substrate processing apparatus having a polishing section, a cleaning section including a reversing machine for reversing the substrate and a plurality of cleaning devices (42, 43, 44, 45) for cleaning the substrate which has been polished, and a transferring mechanism for transporting the substrate from the polishing section to the cleaning section, said method comprising detecting a malfunction in any of the polishing section, the cleaning section and the transferring mechanism said method characterized by: classifying substrates, upon detection of a malfunction in any of the polishing section, the cleaning section and the transferring mechanism, according to the site of the malfunction and to the positions of the substrates in the substrate processing apparatus; and carrying out an operation for each of the substrates after the detection of the malfunction; wherein when the malfunction is detected in the polishing section, said operation comprises; stopping an operation for feeding a new substrate into the substrate processing apparatus and an operation of the polishing section while continuing operations of the cleaning section and the transferring mechanism,recovering the substrates present in the polishing section from the polishing section after all substrates present in the cleaning section and the transferring mechanism are recovered from the substrate processing apparatus by the operation of the cleaning section and the transferring mechanism, inputting an interrupt processing command into another substrate processing apparatus which is in normal operation, stopping transfer of a substrate from a polishing section to a cleaning section in the another substrate processing apparatus in accordance with said interrupt processing command, releasing a lock of a substrate carry-in/carry-out door in the another substrate processing apparatus in order to receive the substrate recovered from the polishing section in which the malfunction is detected in the substrate processing apparatus, and cleaning the substrates recovered from the polishing section, in the cleaning section of the another substrate processing apparatus in which the cleaning section is in normal operation. classifying substrates, upon detection of a malfunction in any of the polishing section, the cleaning section and the transferring mechanism, according to the site of the malfunction and to the positions of the substrates in the substrate processing apparatus; and carrying out an operation for each of the substrates after the detection of the malfunction; stopping an operation for feeding a new substrate into the substrate processing apparatus and an operation of the polishing section while continuing operations of the cleaning section and the transferring mechanism,recovering the substrates present in the polishing section from the polishing section after all substrates present in the cleaning section and the transferring mechanism are recovered from the substrate processing apparatus by the operation of the cleaning section and the transferring mechanism, inputting an interrupt processing command into another substrate processing apparatus which is in normal operation, stopping transfer of a substrate from a polishing section to a cleaning section in the another substrate processing apparatus in accordance with said interrupt processing command, releasing a lock of a substrate carry-in/carry-out door in the another substrate processing apparatus in order to receive the substrate recovered from the polishing section in which the malfunction is detected in the substrate processing apparatus, and cleaning the substrates recovered from the polishing section, in the cleaning section of the another substrate processing apparatus in which the cleaning section is in normal operation.