With the sharp rise of functionalities and connectivities in multi-core embedded systems, these systems have become notably vulnerable to security attacks. Conventional software security mechanisms fail to deliver full safety and also affect the system performance significantly. In this paper, a hardware-based security procedure is proposed to handle critical information in real-time through comprehensive separation without needing any help from the software. To evaluate the proposed system, an authentication system based on an image procession solution has been implemented on a reconfigurable device. In addition, the proposed security mechanism is evaluated for the Networks-on-chips, where minimal area, power consumption and performance overheads are achieved.