The present disclosure relates to a pre-5th-Generation (5G) or 5G communication system to be provided for supporting higher data rates Beyond 4th-Generation (4G) communication system such as Long Term Evolution (LTE). Embodiments herein provide method and system for end-to-end security over signaling plane in a mission critical data (MCData) communication system. The proposed method includes various ways of securing MCData data payload transmitted over signaling plane using short data service (SDS). The proposed method allows usage of multiple security keys to encrypt the MCData SDS message as per the requirements. Various Keys such as, signaling plane key or media plane key or a dedicated MCData data payload signaling key can be used independently or in a combination thereof to achieve the desired security context. The proposed method allows protection of all the application level components with the signaling plane security context.