Nyquist wavelength-division-multiplexing (NWDM) systems based on offset quadrature amplitude modulation (OQAM) have been considered as interesting candidates to achieve a better spectral efficiency. However, such systems are very sensitive to laser phase noise that causes the loss of OQAM orthogonality. In this paper, we investigate carrier phase recovery using a modified extended Kalman filter (M-EKF) in OQAM-based NWDM systems. The proposed method can achieve an optical signal-to-noise ratio (OSNR) penalty lower than that of the state-of-the-art modified blind phase search (M-BPS) algorithm. More specifically, for a 1e-5 normalized laser linewidth, the M-EKF method exhibits 0.8-dB and 1.7-dB OSNR penalties (at a bit-error-rate of 3.8×10-3) lower than the M-BPS method for 16-and 64-OQAM modulations, respectively. Furthermore, compared to the M-BPS method, our proposed method is of lower complexity. The required total number of multiplications and additions of the M-EKF method is reduced by about 3.3 and 6.7 times compared to that of M-BPS for 16-and 64-OQAM modulations, respectively, confirming the effectiveness of the proposed method.