"Konbanwa Tokyo! PM @narendramodi arrives in Japan for the Annual Summit, his second visit in two years," External Affairs Ministry spokesperson Vikas Swarup tweeted.
In a pre-departure statement here on Wednesday, Modi said the high-speed railway cooperation between the two countries would boost bilateral trade and investment.
"The high-speed railway cooperation between India and Japan is a shining example of the strength of our cooperation," he said.
"It will not only boost our trade and investment ties, but will also create skilled jobs in India, improve our infrastructure and give a boost to our 'Make in India' mission."
During Japanese Prime Minister Shinzo Abe's visit to India last year, the east Asian economic superpower committed itself to a high-speed railway line between Mumbai and Ahmedabad.
"On November 12, Prime Minister Abe and I will travel to Kobe on the famed Shinkansen -- the technology that will be deployed for the Mumbai-Ahmedabad high-speed railway.
"Both of us will also visit the Kawasaki Heavy Industries facility in Kobe, where the high speed railway is manufactured," Modi said.
Stating that the India-Japan partnership was characterised as a Special Strategic and Global Partnership, Modi said the two countries "see each other through a prism of shared Buddhist heritage, democratic values, and commitment to an open, inclusive and rules-based global order".
"Today, Japan is one of the top investors in India. But many Japanese companies, which are household names in India, have been committed to the potential of Indian economy for several decades," he said.
The Prime Minuster said that in Tokyo he would have a detailed interaction with top business leaders from India and Japan to look for ways to further strengthen trade and investment ties.
He will call on Japanese Emperor Akihito and review the entire spectrum of the bilateral cooperation with Prime Minister Abe in Tokyo on November 11.
Modi, who left New Delhi early on Thursday morning, made a brief stopover in Bangkok to pay homage to the late Thai King Bhumibol Adulyadej, the world's longest-ruling monarch, who died last month.