In this paper, a robust technique is proposed for the estimation of fundamental frequency in unbalanced three-phase power systems. This is achieved by firstly justifying the modelling mismatch inherently overlooked in the conventional complex-valued least squares enhanced smart discrete Fourier transform method, and then applying the total least squares framework to minimise the error vectors corresponding to both the independent and dependent consecutive voltage measurements and, eventually, to achieve higher immunity to both noise and harmonic pollution. Simulations on both synthetic and real-world noisy unbalanced power systems demonstrate the performance advantage of the proposed algorithm over other smart discrete Fourier transform based ones.