As the number of processing cores is increasing dramatically, the communication among them is of high importance. Network-on-Chip (NoC) has direct access to all resources and information within a Systemon-Chip (SoC) by rendering it appealing to attackers. In this paper a novel Hardware Trojan (HT) assisted Denial of Service (DoS) attack, called Greyhole attack is introduced. The HT-Greyhole attack targets the routers within NoC by causing performance decrease and packet loss increase. However, during an HT-Greyhole attack certain packets, which are arriving towards the router, are dropped which makes it hard to detect. In this paper, we design a detection and defense method, against HT-Greyhole attack, which is based on Software Defined Network-on-Chip (SDNoC) architecture. The results demonstrate that by using the proposed defense method the packet loss decreases by 76% under Transpose traffic, 77% under BitReverse and 50% under Uniform traffic.