The present disclosure relates to a communication method and system for converging a 5th-Generation (5G) communication system for supporting higher data rates beyond a 4th-Generation (4G) system with a technology for Internet of Things (IoT). The present disclosure may be applied to intelligent services based on the 5G communication technology and the IoT-related technology, such as smart home, smart building, smart city, smart car, connected car, health care, digital education, smart retail, security and safety services. Accordingly the embodiments herein provides a method and system for ciphering of initial NAS message protection procedure. A UE is registered to a first PLMN and a first 5G NAS security context has been established. The UE selects a second PLMN. The UE sends Initial Registration procedure with only cleartext IE to the second PLMN. The second PLMN may initiate and perform authentication procedure. The second PLMN initiates NAS Security mode control procedure and sends a Security Mode Command message containing the selected NAS ciphering method to the UE. The UE sends entire the Registration Request message containing both cleartext IE(s) and non-cleartext IE(s) using the NAS ciphering method sent in the Security Mode Complete message. The second PLMN send Registration Accept message.