Following talks with his Japanese counterpart Shinzo Abe, Modi said the pair had agreed plans for Japan to build India's first bullet train to slash journey times between the cities of Mumbai and Ahmedabad.
"This enterprise will launch a revolution in Indian railways and speed up India's journey into the future," Modi said of the deal, adding that Tokyo would also extend a $12 billion package of financing and assistance for the train.
"It will become an engine of economic transformation in India."
The two leaders also agreed a long-mooted memorandum of understanding on the peaceful use of nuclear energy, which will be signed once technical details are finalised, a spokesman for India's foreign ministry said on Twitter.
Japan once shunned nuclear cooperation with India, which has not ratified the international nuclear Non-Proliferation Treaty, but analysts say Tokyo has since softened its stance.
The two countries also agreed to explore future projects on defence technology transfer, including on Japanese-made US-2 amphibian aircraft.
Modi also said India would extend visas on arrival to Japanese citizens from next year.
Modi and Abe, both right-wing nationalists, have forged an unusually close relationship since the Indian leader came to power last year, in part to counter China's growing influence.
The Indian PM has pledged to overhaul India's ramshackle railways and other infrastructure as part of his ambitious economic reforms -- an area praised by Abe earlier in the day.
"Prime Minister Modi's economic policies are like Shinkansen -- high speed, safe and reliable while carrying many people along", the Japanese premier said in a reference to the Japanese bullet train.
After a meeting with business leaders on Saturday morning, Modi lauded the recent decision by Japanese-owned carmaker Maruti Suzuki to export Indian-made Baleno cars to Japan.
"For the first time, Japan will import cars from India. And Maruti will manufacture cars here," Modi said.
Tokyo is encouraging Japanese businesses to tap fast-growing emerging markets such as India, as the domestic market shrinks due to a rapidly ageing population and low birthrate.
The two leaders are expected to leave later Saturday for India's holiest city of Varanasi and the premier's parliamentary constituency.
India's economic growth accelerated to 7.4 percent in the second quarter of the financial year, figures released in November showed, outperforming China.
