He will be received by his Japanese counterpart Shinzo Abe at Kyoto airport, who will also hold dinner for Mr Modi later on Saturday.
His earlier visits as PM were confined to the regional countries, Nepal and Bhutan. This tour to Japan is the third bilateral visit after he became Prime Minister in May this year.
He went to earlier Brazil for the BRICS Summit; his only other foreign visit.
Modi hinted about his focus on tour to Japan a day earlier, saying, “In the field of defence and security, I feel time has come for us to upgrade our relations. I see in the recent changes in Japan’s defence export policies and regulations a possibility to engage in a new era of cooperation in high-end defence technology and equipment”.
While interacting with the Japanese media on Friday, he said, “There has been significant progress in our negotiations on the civil nuclear agreement; on the US-2 amphibian aircraft; and in the field of high speed railway. It is my hope that my visit this time will pave the way for concrete cooperation on these fields.”