This paper investigates an enhanced field-oriented control method for a two-pole surface permanent magnet synchronous machine (PMSM) with a symmetrical nine-phase winding configuration and a single neutral point. Magnets on the rotor are shortened, reducing cost of the machine, but cause production of highly non-sinusoidal back-electromotive force (EMF). FFT analysis of the EMF reveals a high third harmonic component, which is almost equal in magnitude to the fundamental. By investigating possible torque improvements using FEM software simulations, it was shown previously that, if controlled under optimal third harmonic current injection, the electromagnetic torque of the studied PMSM can be improved by up to 36%. The optimal current harmonic injection ratio between the fundamental and the third harmonic is determined first in this paper, using the maximum torque-per-ampere method (MTPA). An enhanced high-performance field-oriented control (FOC) algorithm to control a nine-phase non-sinusoidal back-EMF PM synchronous machine is devised next. The developed improved control algorithm is verified using simulation studies and further validated using an experimental prototype.