Reconfigurable architectures are being increasingly widely used thanks to their high flexibility. This flexibility is due to their inherent ability to reconfigure (whether dynamically or not) functional blocks. Many configurations can be used and changed while the application is running in the reconfigurable system, and/or the same configuration can be used by several systems at different times. The flexibility of reconfigurable systems is greatly enhanced if they can be reconfigured remotely. But in the case of remote reconfiguration, security is of paramount importance. In this article, the problem of remote configuration is addressed by the concept of disposable configuration, an efficient, secure and reliable mechanism for maintaining the flexibility and security of the system. For the implementation of the secure reconfiguration protocol, we propose to use the secure-by-design HCrypt cryptoprocessor, providing low cost, high level protection against both hardware and software attacks without configuration throughput reduction. We validated the approach on a Xilinx Virtex-6 FPGA but it can be easily mapped to any other FPGA or SoC.