Modi flew to Tokyo this evening after an overnight stay in the historic city of Kyoto where he visited two ancient Buddhist temples with Abe accompanying him in a significant gesture.
During his hectic schedule in Kyoto on the second day of his five-day visit to Japan, Modi also sought Japanese help to fight the deadly sickle cell anemia commonly found among tribals in India when he went to the Stem Cell Research Facility of the Kyoto University and got a positive response.
63-year-old Modi and 59-year-old Abe, who share cordial relations and hit it off well in Kyoto, will have a substantive summit agenda.
A new chapter is expected to be opened in India-Japan ties when the two leaders will focus on enhancing cooperation in the fields of defence and infrastructure besides boosting trade and investment.
The two sides are expected to agreed to launch a security consultative framework involving their foreign and defence ministers and sign an agreement to jointly produce rare earths that could be exported to Japan, while discussing ways to elevate the Strategic and Global Partnership to a new level.
Japan already has a security consultative framework with the US, Australia, Russia and France.
"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," Modi had said in an interview to Japanese media ahead of the visit.
Discussions are also expected to focus on civil nuclear cooperation and help by Japan in improving Indias infrastructure, particularly the railways, and cleaning of river Ganga.
On the second day of his visit, Modi, clad in all-white kurta pyjama, sleeveless jacket and white sandals, offered prayers at the two prominent Buddhist temples in Kyoto Toji and Kinkakuji.
He first went to Toji Temple, which is inspired by the trinity of Brahma, Vishnu, Mahesh of Hindu philosophy and is a World Heritage site.
Modi was at the temple complex for about half-an-hour during which he enquired about the history of the eighth-century Buddhist pagoda.
While leaving the complex, Modi thanked Abe for accompanying him to the temple and spending time with him.
Abe, on his part, told Modi that this was only the second time that he had visited Toji temple, the last being during his student days.
Abe had specially come to Kyoto from Tokyo to meet Modi and be with him. The Japanese Prime Minister rarely greets a foreign leader outside the national capital.
In Kinkakuji, Modi mingled with tourists and visitors, shook hands, pulled ears of a child and posed for photographs with groups of people.