The control segment in satellite navigation systems is responsible for estimating satellite orbit and clock bias which is required for a reliable Position, Navigation and Timing (PNT) user service. Initial orbit determination is a crucial step which accounts for all unknowns/anomalous parameters such as satellite orbit manoeuvres, on board and receiver clock frequency variations and environmental effects. It is vital that the estimates of the orbits and clock are insensitive to these factors. In this paper, an initial orbit determination method is presented using existing robust methodology for estimation of initial satellite position and its propagation using a variant of the Kalman Filter (KF) which allows the initial position determination process to be independent of satellite and receiver anomalies. The derivation of this KF variant is presented. Preliminary results obtained from simulated data are shown. The said method is checked for robustness by comparing results obtained for a given satellite position data set with that from the conventional Kalman Filter. The conventional KF exhibits divergence due to anomalies which are eliminated by the use of the method presented in this paper.