Prabhu will also visit South Korea to explore the possibilities of acquiring high speed technology for the Railways' ambitious bullet train project.
While railways is facing an increased number of train accident in the recent past, Japan is known for zero accident rate in its rail operation.
Besides, Japan is involved in the construction of Western Dedicated Freight Corridor and railways is in the process of importing 40 high power electric locomotives from it.
Minister is expected to discuss the issues affecting railways and also ways to strengthen cooperation in rail sector with Japan and Korea, said a senior Railway Ministry official.
Accompanied by Railway Advisor (Infrastructure) Girish Pillai, Prabhu is also expected to witness the modernised signal system and experience high speed service in both the countries before returning on September 13.