In this study, an extended Kalman filter (EKF) for estimation of spacecraft's position and velocity by single station antenna tracking data in the presence of singularities is proposed. The designed EKF estimates the position and velocity of the spacecraft on direct nonlinear range-azimuth-elevation measurements. The proposed EKF is examined through the geostationary satellite orbital motion simulations. The corruption in the results by EKF emerges from singularities caused by the highly complex elements of the Jacobian measurement matrix. The recommendations to prevent the mentioned problem are given.