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We focus attention on the development of security techniques using software defined radio (SDR) technologies. We propose a new secure download system which uses the characteristics of the field programmable gate arrays (FPGAs) composing the SDR. The proposed system has the novelty that realization of high security encipherment is possible. This is achieved using the characteristic of FPGAs which allows systems to be arranged in a variety of different layouts, as well as by using the configuration information as the key. This unifies the renewal of the key and the encipherment. In addition the proposed system has the merit that it has high security against illegal acquisition such as a wiretapping, and can also be used in conjunction with any other current cipher algorithm. As an evaluation of the security, we show that the proposed system has high immunity to illegal acquisition of software using replay attack, by verification of the protocol as well as by numerical computation. The proposed system can therefore realize high security software downloads based on SDR.