This study investigates a real-time fault diagnostic of a transportation system which needs two drives with fault-tolerance capabilities. Owing to the constraints on the mass of the system and on the cost of the voltage source inverter, a drive with two six-phase permanent magnet synchronous machines in series-connection supplied by two six-leg inverters is chosen. Despite the serial connection, independent control of the two machines and fault-tolerance to open-switch fault is ensured. Nevertheless, a fault detection identification (FDI) process is required for analysis and/or control reconfiguration. The proposed FDI is based on the combination of different criteria obtained from the two zero-sequence currents and from the normalised currents mapped into two frames defined by the concordia transformation. Results obtained from simulation and experimental tests show the effectiveness of the proposal.