© 2016, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.A sea skimming missile is needed to be flown above mean sea level as low as it can, in order to decrease detectability; so that, survivability of the missile against counter attacks of the target ships is maximized. On the other hand, flying at very low height is a tough task under disturbances due to sea waves and measurement errors of various sensors used in height control loop. Thus, a robust altitude control system design is the main challenge among the other control algorithms for a sea skimming missile. In this paper, extended Kalman filter based altitude controller method is proposed and compared with the existing designs in literature. Simulation results under a few scenarios, in which sensor errors, severe sea conditions, and limited computing power are taken into account, are shared. Results show that the extended Kalman filter based altitude controller has satisfactory performance against many real world issues.