Contentions can degrade the performance of communication significantly on network topology like 3D-Mesh/Torus. On these topologies, it is important to establish a method for predicting penalty of contentions to enable precise and fast tuning on communications. For example, techniques of tuning such as choosing dynamically faster algorithm of collective communications or finding appropriate task-allocation depends on the preciseness of the performance prediction. This research proposes a method for predicting a penalty of contentions by using detailed analysis of packet priority on direct interconnection network. Usually, the penalty of contentions is predicted by counting the number of communications issued on the same link at the same time. However, the actual amount of delay caused by contentions depends on the way of arbitrating messages. The message is divided into the packets and transmitted. Then, the contentions between those packets are arbitrated by applying the priority to each packet. Therefore, when the contentions occur, the message which has a lower priority is blocked. By considering these priorities, the method proposed in this research becomes to predict the penalty of contentions more accurately and faster. In the evaluation experiment, the penalty of contentions predicted without considering packet priority is the twice or more than it predicted by simulation. On the other hand, the proposed method of predicting the penalty of contentions is predictable in the accuracy within 20% against simulation. Moreover, the prediction by proposed method is possible to execute it enough at short time.