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With the current evolution in run-time reconfigurable computing, runtime reconfigurable platforms are becoming increasingly viable. End users can download an updated version of a bitstream over the Internet and reconfigure the hardware platform partially without affecting the rest of the system like downloading and installing software. However, remote downloading and upgrading of bitstream is vulnerable to spoofing and replay attacks. This paper presents a framework to guarantee a secure and efficient remote updating of FPGA bitstream on runtime reconfigurable embedded platforms which consist of an embedded microprocessor and a runtime reconfigurable FPGA hardware. The framework addresses different issues including bitstream management, compression, encryption and authentication. A prototype system based on Xilinx Spartan-6 LX45 FPGA Altys board is used as a proof of concept for our framework.