The fast development of quantum computers represents a risk for secure communications. Current traditional public-key cryptography will not withstand attacks performed on quantum computers. In order to prepare for such a quantum threat, electronic systems must integrate efficient and secure post-quantum cryptography which is able to meet the different application requirements and to resist implementation attacks. The NTRU cryptosystem is one of the main candidates for practical implementations of post-quantum public-key cryptography. The standardized version of NTRU (IEEE-1363.1) provides security against a large range of attacks through a special padding scheme. So far, NTRU hardware and software solutions have been proposed. However, the hardware solutions do not include the padding scheme or they use optimized architectures that lead to a degradation of the security level. In addition, NTRU software implementations are flexible but most of the time present a low performance when compared to hardware solutions. In this work, for the first time, we present a hardware/software co-design approach compliant with the IEEE-1363.1 standard. Our solution takes advantage of the flexibility of the software NTRU implementation and the speedup due to the hardware accelerator specially designed in this work. Furthermore, we provide a refined security reduction analysis of an optimized NTRU hardware implementation presented in a previous work.