Network security is the key challenge in IoT. Possible source for security issues and vulnerabilities in IoT networks are caused due to its dynamic network topology, mobility and weak physical security of low power devices. Authentication, Authorization and Access control are important and critical functionalities in the context of IoT to enable secure communication between devices. It is infeasible to use conventional cryptography in IoT networks since security and privacy of critical data are crucial. In this paper, a secure and efficient authentication mechanism in IoT based healthcare system is proposed. Security and privacy of patients‟ medical data are crucial for the acceptance and ubiquitous use of IoT in healthcare. Primary focus of this work is to provide a Multilayer Security using Linear Programmable Pre-coded Matrix Decomposition (MS_LPMD) method for secure authentication and authorization of remote in or out patients. The proposed architecture uses an efficient and secure key management scheme between IoT node and IoT s_gateway. In this approach during the pre-authentication phase, connection between IoT node and IoT secure gateway is established. The Secure Gateway being the primary authentication server validates unique pattern coefficients generated using LPMD process against the coefficients received from IoT Node for authentication. Authenticated IoT Node employs a simple light-weight computational process for cipher key generation used for subsequent encrypted data communication through a secure communication channel. Proposed MS_LPMD scheme is built to protect the confidentiality, integrity and availability of network data by making the system reliable and protecting the system from malicious attacks which can lead to information disclosure. The proposed MS_LPMD approach has outperformed other existing approaches such as AES, EDCH etc, in terms of higher security level and trust worthiness factor. The performance analysis revealed that our proposed MS_LPMD approach has less communication overhead and latency between the IoT Node and secure gateway. Using software-hardware co-designed IoT test bed, the computed results on standard simulation setup shows an average reduced overhead of 29% and latency of 21% when compared to existing EDCH scheme. © Research India Publications.