The satellite communication is embellished constantly by providing information, ensuring security, and enables the communication among huge at a particular time efficiently. The satellite navigation helps in determining the people's location. Global development, natural disasters, change in climatic conditions, agriculture crop growth, etc., are monitored using satellite observation. Hence, the satellite includes detailed information data, and it must be protected confidentially. The field of the satellite is enhanced at an astonishing pace. Satellite data play an important role in this modern world; hence, the onboard-satellite data must secure through the proper selection of error detection and estimation schema. Lightweight deep learning algorithm based on Extended Kalman Filter (KFK) is proposed to detect and estimate onboard pointing error such as an error in attitude and orbit. The Extended Kalman Filter (EKF) is widely used in the satellite system. EKF is utilized in this proposed model to detect the onboard pointing error such as attitude and orbit determination. An autonomous estimation of orbit position is possible through space-borne gravity. The information obtained through the observation of satellite data is compared with the accurate gravity model in detecting the error. The utilization of EKF reduces the dependence of the ground tracking system in satellite determination. The orbital altitude and orbital position are the most important challenges faced in the satellite determination system. The satellite model using the Extended Kalman Filter is an optimum method in estimating the orbital parameters. The errors in the linearization process are detected, and this can be overcome through the proper selection of linear expansion point with the EKF algorithmic model with the Jacobian matrix calculation. The results show that the EKF implementation helps in attaining better accuracy than other methodologies. Its contribution is enormous to many space missions, autonomous rendezvous and docking for manned and unmanned missions (e.g., ISS operations and beyond, in-orbit servicing, and in-orbit refueling), routine satellite OD operations, orbital debris removal systems, Space Situational Awareness (SSA) operations, and others.