"A rare audience that symbolizes the unique warmth between #IndiaJapan. PM @narendramodi greets His Highness Emperor Akihito of Japan," External Affairs Ministry spokesperson Vikas Swarup tweeted.
"Speaking of civilizations. PM @narendramodi and Emperor Akihito talk of the common bonds of #IndiaJapan and the future of Asia," Swarup said in another tweet.
Modi, who arrived here on Thursday, is scheduled to participate in two bilateral business meets here before joining Japanese Prime Minister Shinzo Abe for the bilateral summit later in the day.
On Saturday, Modi and Abe will travel on the Shinkansen high-speed rail to Kobe. During Abe's visit to India last year, Japan committed itself to the development of a high-speed rail link between Mumbai and Ahmedabad.
This is Modi's second visit to Japan in two years.