Modi and his entourage will touch down at Kyoto airport where Japanese Prime Minister Shinzo Abe will receive the Indian head of government.
"My visit to Kyoto reflects the ancient foundations of our contemporary relations and will also focus on some of our nation's priorities, including urban renewal and smart heritage cities as well as advanced scientific research," Modi said in a pre-departure statement Friday.
"I am confident that my visit will write a new chapter in the annals of relations between Asia's two oldest democracies and take our strategic and global partnership to the next higher level," he said.
The Japan visit is PM Modi's first bilateral trip outside the subcontinent
"Japan is one of our closest partners in political, economic, security and cultural realms. It is a key regional and global partner for us. Between our countries, there is only goodwill and mutual admiration," the prime minister said.
"We will explore how Japan can associate itself productively with my vision of inclusive development in India, including the transformation of India's manufacturing, infrastructure sectors, energy and social sectors," Modi said.
"We will discuss how to boost our defence and security cooperation, including in defence technology, equipment and industry, in line with the evolving domestic policies of the two countries. I will try to accelerate progress on the unfinished agenda of projects and initiatives that our two countries have embarked upon," he said.
Modi said he was "keenly" looking forward to the three-day visit to Japan at the invitation of "my good friend, Prime Minister Shinzo Abe, for the annual summit between India and Japan".
"This will be my first bilateral visit outside India's immediate neighbourhood as prime minister of India, which underlines the high priority that Japan receives in our foreign and economic policies," he said.
The prime minister said this was a reflection of Japan's paramount importance in his vision for development and prosperity in India and in peace, stability and prosperity in Asia at large.
"Japan is one of our closest partners in political, economic, security and cultural realms. It is a key regional and global partner for us," he said.
Abe will be hosting a dinner for his Indian counterpart later Saturday.
This is Modi's third official bilateral visit after becoming prime minister in May this year. He made bilateral visits to South Asian neighbours Bhutan and Nepal after becoming prime minister.
The only other visit he made abroad after assuming the top post was Brazil for the BRICS (Brazil, India, China, Russia, South Africa) summit.