During his three-day stay here, Modi will hold talks with Abe tomorrow to bolster bilateral security and economic ties.
The two leaders, who share cordial relations, will have substantive summit meeting during which they will look at ways to take the Strategic and Global Partnership forward.
Modi has a substantive agenda during the trip which he hopes will "write a new chapter" in bilateral ties and take the Strategic and Global Partnership to a higher level.
Cooperation in the fields of defence, civil nuclear, infrastructure development and rare earth materials is expected to top the agenda of the discussions.
Some agreements, including in defence and civil nuclear sectors, are expected to be signed. Among the agreements to be signed is one on joint production of rare earth materials.
"I am keenly looking forward to my visit to Japan at the invitation of my good friend, Prime Minister Shinzo Abe, for the annual summit between India and Japan," Modi said in his pre-departure statement.
Noting that this will be his first bilateral visit outside the immediate neighbourhood as Prime Minister, he said it underlines "the high priority" that Japan receives in India's foreign and economic policies.
"It is also a reflection of Japan's paramount importance in my vision for development and prosperity in India and in peace, stability and prosperity in Asia at large," Modi said.
"I am confident that my visit will write a new chapter in the annals of the relations between Asia's two oldest democracies and take our Strategic and Global Partnership to the next higher level," he said.
During his two-day stay in Kyoto, Modi witnessed signing of a pact under which his constituency Varanasi will be developed as a 'smart city' in partnership with the Japanese city, which is a confluence of heritage and modernity.
Abe had specially come to Kyoto from Tokyo to meet Modi and be with him. The Japanese Prime Minister rarely greet a foreign leader outside the national capital.
On the second day of his Japan tour, Modi today offered prayers at two prominent ancient Buddhist temples in Kyoto and sought help from a Japanese Nobel Prize-winning stem cell researcher to develop a treatment for the Sickle Cell Anaemia, the deadly disease commonly found among tribal people in India.
In Kinkakuji temple, the Prime Minister mingled with tourists and visitors, shook hands, pulled ears of a child and posed for photographs with groups of people.
He began his day with a visit to the ancient Toji Temple, which is inspired by the trinity of Brahma, Vishnu, Mahesh of Hindu philosophy. He was accompanied by his Japanese counterpart Shinzo Abe when he went around the famous temple which is a UNESCO world heritage site.