We propose a new two-stage digital signal processing scheme to suppress the phase distortion that arises from imperfect pump counter-phasing in a dual-pump fibre-based optical phase conjugation system. We demonstrate experimentally and numerically a signal-to-noise ratio improvement of more than 4 dB relative to conventional phase noise compensation, when the proposed scheme is used with 16/64/256 quadrature-amplitude modulation signals at pump-phase mismatch values as large as 8°.