In this paper, a reliable control system structured with dual CPU modules and dual I/O modules is implemented as a means of achieving a highly reliable fault tolerant control system. For this, faults in the system modules are first examined, and a fault detection technique consisting of self diagnostic, comparison process, and exception processing is applied. Self diagnostic is used to locate which components in the modules have been failed, while comparison process is to cmpare control outputs computed by both CPU modules and protect the plant from malfunction by blocking failed control outputsin advance. Finally exception processing is used to determine the faults that are not detected immediately by the self diagnostic and comparison process, e.g. bus error processing when acknowledge signal for data transfer is not activeted in the I/O modules. Also reliability analysis is conducted for the discrete time Markov model with dual structure. It is shown quantitatively that the reliability is improved in the control system with dual structure in comparison with a system with single module structure.