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BeiDou Navigation Satellite System (BDS) is composed of satellites in geostationary Earth orbit (GEO), medium Earth orbit (MEO) and inclined geosynchronous orbit (IGSO). However, the orbit determination of geostationary Earth orbits and of geosynchronous orbits (GSO) with small inclination angle and small eccentricity is a challenging task that is addressed in this paper using Extended Kalman Filter (EKF). The satellite positions were predicted in Earth-centred inertial (ECI) reference frame when propagated through Keplerian model and perturbation force model for different values of right ascension of ascending node (RAAN). Root mean square (RMS) errors of 9.61 cm, 6.73 cm and 11.46 cm were observed in ECI X, Y and Z satellite position coordinates of GSO respectively, whereas, the RMS errors for GEO satellite were 8.89 cm, 7.92 cm, and 0.93 cm respectively in ECI X, Y and Z coordinates; for perturbation force model with maximum value of RAAN when compared with dynamic orbit determination model. Kolmogorov-Smirnov test for EKF reported a p-value > 0:05, indicating a good fit of perturbation force model for orbit propagation. Orbit determination using EKF with perturbation force model were compared with that using EKF with Kepler's model. Wilcoxon Rank Sum test was used to compare the residuals from EKF algorithm through Kepler's model and perturbation force model. EKF with Perturbation force model showed improvement in predicting the satellite positions as compared to Kepler's model. EKF with Perturbation force model was further applied to International GNSS Service (IGS) station data and kilometre level accuracy was achieved. RMS errors of 0.75 km, 2.53 km and 1.91 km were observed in ECI X, Y and Z satellite position coordinates of GSO, respectively, whereas, the RMS errors for GEO satellite were 3.89 km, 4.20 km and 6.66 km respectively in ECI X, Y and Z coordinates for perturbation force model. [ABSTRACT FROM AUTHOR]